Your qualm seems to be with the perception of your former Employer/Colleagues, however, it seems like within your question you have somewhat answered it when you say that your Boss hasn't brought it up to you as an issue.
Your Boss may in fact be very hands-off but in a situation where an employee is considered to be abusing their time off they would have no choice but to confront you if it were actually an issue. It's true styles and techniques vary somewhat when it comes to management, but there's none that I've ever seen, heard of, or would believe exists where a Boss would refrain from commenting on a matter as important as attendance. I think you are absolutely fine in this regard.
To put your mind at ease I can think of two different approaches to this issue.
Request a medical note from your Physician and bring it into your place of employment. You would usually file this note with HR, but I would make it a point to politely ask my Boss(through e-mail, phone, face to face) what the procedure is to turn it in. This gives you an air of responsibility and implies that the days off were honest and necessary. No one should hold that against you.
Simply talk to your Boss. Go down to her office, knock on her door, and say "Hey Boss Lady! I just wanted to let you know that I really appreciate all the time off that I've had due to illness. It means a lot that I can take time off when I really need it." And, if you're absolutely resigning, places usually conduct exit interviews but you can, again, just stop by your Boss and explain "I realize that this is unusual timing, seeing as I've been so ill lately and everything, but I just wanted to let you know that I'm grateful to have worked for this company. I just found a new opportunity, that's all."
Honesty probably is the best policy in this situation, but do with my advice what you will. As far as your colleagues are concerned, you can't really help what they're going to think. If they're professional they'll understand.
All in all I think you're probably making too big a deal out of this. People come and go in all companies and the timing is hardly ever perfect. Do the best you can to make the switch easier, but at the end of the day, it really doesn't matter what they think about your leaving and I would venture to say that they are less critical of your actions than you think.