He made his understanding about violence being used against him if the Thug didn't get his money back, so why not pay him back with his early winnings? I would think that'd be the first thing on his list so as not to piss the thug off to the point of murder.
He should have poisoned the NZT pills prior to giving them to the thug. It would have solved his problems. He ended up having to kill the goons later on anyways.
I wondered that myself, and rationalized it this way. Keep in mind it's just my thoughts, and just a theory.
I think the movie's central theme deals with among other things, addiction, especially to power/money. He saw early success, and instead of paying his loan shark off quickly, his new mental powers made it possible to see potential for more quick income if he acted on it fast. If he paid the goons, his capital wouldn't be as good, and would take longer. He wanted more and more, like an addict.
It's like when you go to a casino with $20, and tell yourself you'll play 'til that's gone then go home. when you are down to the last few dollars, say you hit for $50. You should be rational and go home at that point, but casino owners know most people won't. They will rationalize spending more in the hopes of hitting again.
This is definitely a plot hole. The book handled it better. In the book, the thug found the pills on his own when he went for the first payment. He only found the few that Eddie kept on hand in the tin on his desk.
When Gennady went back for the second payment, Eddie tried to pay him back the entire amount but Gennady refused and insisted on only the weekly payment so he would have to keep coming back every week and then blackmailed Eddie for 10 pills a week (Eddie said he could only get that many).
In the book, Eddie tried to pay the gangster back with a cheque, and the guy was like "Do I look like a bank manager? I want cash!". Eddie ended up getting sidetracked with some other crap, which led to him forgetting to pay the man back.