Doing the right thing is eating me alive. Opinions?

Long story short. Working on a thesis with a girl. She just came out of an abusive relationship. Things just happened between us with no effort from either party. After like 7 months of being together she went back to that ass-hole because he pretended to change for like literally 3 days, then went back to being himself. She is determined to make it work somehow.

I accepted her decision but we used to have fights not related to work every week. She would start it and I would make it worse since I stopped putting in all that effort to remedy things no longer seemed justified since we were no longer together. After about a month of this I decided to work alone, since this headache was also not justified.

After more then a month of having a shitty time getting over her (0 progress) she called because she wanted to continue working. "Me: We can work as long as we don't fight about things outside of work". Because it was the right thing to do.

I have 0 self control around her. I say and do things without even deciding to, things that are not necessarily inappropriate but shows that I clearly have a big chunk (all) of my soft corner left for her. Can't say no to her, she has already put in effort and also made a point to approach me to continue working, which is very uncharacteristic of her, so she must need it. Can't stop working myself, this thesis is very important to me for a myriad of reasons. And I don't know how I am going to manage this situation. Not strong enough, not mature enough.

Everything in life is going according to plan, don't waste time sulking around, but I am sad by default. Work will continue for 8 months more at least. And I am so emotionally distressed that in the worse case scenario I think to myself that I shall wait till its actually time to get married then approach her because her current story is never going to work out and will surely end by then.
Doing the right thing is eating me alive. Opinions?
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