People worry about overqualified candidates because there is a chance they will leave once they find a better paying job more fitting of their skill set (or they are worried about you gunning for their role later on, though this one is not common I have seen it).
If the company or interviewing manager does not ask about why you are applying for a position you are overqualified for then do not mention it. On that note you may also want to tailor your resume to be more geared towards the role you are going for and leave out some of the higher level stuff as to not appear overqualified. Just make sure you leave enough in the resume to get an interview.
If they do ask then express what you have said here. "I am willing to be flexible about the salary as it is not my primary objective." and that you have been on a break for a few years are are only looking to get back into the market and are willing to start off at a lower level then when you went on break. This is not so uncommon that it is a red flag or anything. I actually had a similar experience myself. They did mention I was overqualified but I made sure they understood my reason for accepting a lower level position and insured them I would not just up and leave any time soon.
Will companies consider hiring an overqualified person for a junior position provided the candidate is ready to work for the same salary offered for the junior position?
This does depend on the company of coarse but for the most part the answer is yes. Companies do hire people who are over qualified all the time and offer that person the same salary range that position qualifies for. It is up to you to decide if you will accept that offer.
Can I apply for slightly lower level positions that need about 5 to 7 years of programming experience?
Simple answer: Yes
You can apply for whatever you want to apply for. It does not mean you will or wont get an interview but there is no reason you cannot apply for a position you have the skill set to perform. Just because you have a few year more than what they are looking for does not imply you should not apply for the position.
I would like to know if there are reasons I may be disqualified other than salary?
This question is a lot broader than the issue of over qualification. Maybe change this question to be more specific.
One can be disqualified for many reason. Could be personality clash with the company/interviewing manager. Could be a failure to answer some of the question correctly. Could be a simple matter of someone else being a better fit. And so on.