First off, I can tell from your post that you have a lot of passion and are emotionally invested in your workplace. That can be a great thing, and I don't want to tell you to change that. Let's focus on your concerns, as you've laid them out in your post. BTW, If I missed the mark and did not correctly identify your concerns, please let me know in the comments so that I can correct myself.
You are concerned about project delays
I assume that this concern stems from fears about what will happen if a project gets delayed too much. First, it's important to accept that projects will get delayed due to illness or other circumstances outside of your control. It's inevitable. Make peace with it. Heck, even better than making peace, make contingency plans, if you can.
Anyway, it sounds like you are not being chewed out by your boss for the delays. In fact, you are being praised for giving what is probably more effort than is expected of you. If that's all true, and these delays aren't about to bankrupt the business and cost you your job, then there is no material reason to stress yourself out about it or to strain yourself or others in order to prevent the delays.
If you are actually being chewed out for the delays but just didn't mention it, then you should make a paper trail that explains the cause of the delays (e.g. Employee X was out for 2 weeks, reducing our velocity by N%) and then discuss it with your boss. But, keep that separate from the matter of the feedback you've already gotten.
You are concerned about another person's work ethic
I'm not going to be able to sugarcoat this for you. There are two problematic thought patterns behind this:
- You feel compelled to work very hard despite it giving you very little material benefit (all it seems to have done is net you some praise.)
- You feel that your coworker is not holding himself to the same standard as you, perhaps you even feel that he is lazy or is getting undeserved preferential treatment.
You should challenge your thinking on these matters. The second item is a good example of crab mentality. Whether or not your coworker has "legitimate" reasons to be late or take lots of vacations should be irrelevant to you unless it is causing you material harm. And, as I said in the section before, that doesn't mean delays; it means you getting (hypothetically) chewed out for delays.
In fact, even though you are middle management, you should still recognize that as an employed worker, you are a sucker if you work yourself harder than what your pay is worth. Praise does not pay the bills. I'm not saying to slack off, but you should understand that if you choose to work harder than what your pay is worth, that's on you.
You are concerned about being perceived as the bad guy, for doing what you think is right
This is totally understandable. You care a lot about your workplace! You want the company's projects to succeed. You have good intentions, no doubt.
There's just one little problem: there are more people on this earth who have this concern than there are people who are in the right in whatever conflict they're concerned about. Sometimes you're the bad guy, sometimes the other guy's the bad guy, sometimes both of you are bad guys, and most often, nobody is the bad guy, you're just well-intentioned people who aren't seeing eye-to-eye. And all of this is based on perspective, not whether someone is right or wrong in their beliefs. Sometimes, well-intentioned people do harm to others without meaning to: for example, a passionate colleague who works much harder than they need to tries to push their sense of passion onto others, and, when it isn't reciprocated, treats the people around them as if their lack of passion is something audacious. That just might get others to perceive them as a source of persecution–a bad guy.
If you don't want to be perceived as a bad guy, then you should take care not to do harm to others, and if you do, sincerely apologize about it–but don't flagellate yourself over it, either. Mature adults will recognize your sincerity and be more willing to work with you to find ways to resolve conflicts. Be sympathetic to others' thoughts and feelings. And, if someone is acting in a way that you can't interpret as being well-intentioned, first question whether you lack some critical information that is preventing you from seeing their good intentions. In general, you could try talking to them or people who know them about your concerns (of course, in a non-judgmental way, preferably even in a roundabout way that doesn't let on that you're suspecting malice.)
In this particular case, though, that ship has sailed, so you're probably better off just taking it for granted that your colleague is well-intentioned, apologize, and move on. Seriously. Even if he's actually a cartoonish jerk who's slacking off just to try to make your life miserable, in this particular case, you missed your opportunity to have a well-intentioned discussion when you expressed surprise to your colleague about them taking more time off. If you want to avoid looking like a bad guy, then you should assume he's not one either, and treat him nicely.
You are concerned about criticism of your personality/personal attitudes being non-constructive
Personality issues are real, lots of people have them, and it all comes down to whether your personality/personal attitudes are causing harm to yourself or others. If they are, then criticizing them can be constructive, especially if the criticism offers advice on how to change your mindset, or ideas on what you could have done differently, or insight into your subconscious motivations behind your behavior. It is what I have been doing in this post.
If you receive negative feedback about your personality or personal attitudes a lot, then you might want to see a therapist about it. I think Cognitive Behavioral Therapy, or even better, Dialectical Behavioral Therapy, can be useful even when you aren't trying to treat a mental illness. At the end of the day, if your thoughts/feelings are influencing your actions in a negative way, you can use therapy to change your habits. And DBT in particular can even change entire aspects of your personality, for the better. If you feel like these kinds of problems are recurring in your life, I sincerely recommend you consider a therapeutic approach.
Apologies for the verbose post. I hope it was useful to you regardless.