Tommy befriended Rusty because he had money. He latched on to him like a parasite, and even though Rusty is the one to suggest starting a fraternity, it looks a lot like Tommy was leading him towards that thought with the "I told you so" about the Preps, and then dismissing the Jocks and Nerds as viable frats to join. It's as though he was saying without saying, "Oh, if only there was a way to set up our own frat, but for that we'd need money and where, oh where, are we going to get that?" *wink-wink*. It feels quite manipulative, like he's using Rusty to get something that he (Tommy) wants.
Obviously, he is. The catch is that he's getting something Rusty wants, too. At a certain point you can't really call that manipulation.
After all, the MC is only pledging the DIKs to have a roof over his head. He was happy to mooch off Rusty same as the rest. Now, you can say he was willing to do work to repair the mansion when Tommy just wanted someone else to fix it, but I say that's just a result of the MC being smarter than Tommy. Tommy being a whiny bitch has never been in question. If Rusty had enough money to repair the place, would the MC have insisted he and his 'brothers' do the work themselves anyway? Doubtful.
And it's not like the MC was offering to patch up the mansion for the DIKs on his own. In the end, his big speech conveniently resulted in the DIKs agreeing to pitch in to help solve the MC's problem. So shall we conclude that the MC is manipulating the DIKs too?
If we want to see actual manipulation, I think Quinn is a better choice. Unlike Tommy, she deliberately lied to Sage so that Sage would do something she never would have done on her own. Moreover, the end result of Sage's sacrifice was supporting a cause Quinn knew Sage would not approve of. Quinn even tried to goad Sage into getting more money by submitting to her parents.
That is what taking advantage of a rich friend looks like.
To me, the difference between the MC and Tommy is much smaller than the difference with Quinn. Tommy is lazy and headstrong, so he feels no shame in mooching. But he doesn't trick his marks. He takes whatever he gets just by being himself. You'll note that when he says he considered Quinn an even closer friend than Rusty, the context is not that Rusty is no longer a close friend; it was meant to illustrate just how close he felt his bond with Quinn was.
Similarly, when Vinny said Tommy and Rusty should pass their own hazing rules Tommy was initially insulted, but by the time they were picking tasks on the roof Tommy was enthusiastic even knowing he'd have to do them. Clearly his interest in bonding with frat brothers outweighed the missed opportunity to demean people in his mind.
I understand your dislike for Tommy. I even share it. But I think you are going to far when you assume that ALL his motivations are not merely self-serving, but must harm those around him as well.
