She can not get alimony simply because he is living with you, however she is in the process of setting up a good status quo situation for herself. While she will have to get a job once they are divorced she is in the process of proving she can't make it without his help and he is in the process of proving he CAN make it while helping her. If him paying her keeps her off assistance what do you thnk the courts are going to do?
Is this agreement he made filed with the courts? If not then he needs to quit paying immediately. She is out so if nothing is CO'd (an agreement filed with the courts would be considered court ordered if a judge signed off on it) then he could be in control right now. Has divorce been filed for or just separation? If not he needs to get on that ASAP.
Her son's sexuality is not part of the equation. She could be the most moral person in the world and have a bi-sexual child. Him living in her home is not up for discussion. He is 15, she can't kick him out. (The girl on the other hand is a different story) Since her husband is living with another woman it makes her living with another man a wash.Being there is no co-habitation clause or morality clause he can't even bring it up if the separation agreement is CO'd. Except in the case of the temporary alimony....he may be able to bring it up for that but the agreement was for a year. He will spend 5 months trying to get into court to change it.
She can definitely TRY to get life time alimony (not based on him living with you). She's not going to get it for a 6 year marriage. She may get it short term though, although probably not at the amount of what he's paying for now.
That said it amazes me that when one person is already living with someone they complain about their stbx doing the exact same thing. It also amazes me that people who are barely separated and not even divorced are ready to jump into another relationship. My advice to you (even though you didn't ask for it) would be to distance yourself emotionally. He has a lot to go through and isn't even close to healing yet from his marriage. I know you won't listen because no one ever views themselves as a rebound. Just keep it in the back of your mind.
When we were together, you said you'd die for me. Now, I think it's time you kept your promise.