I think you're right about the money ... that was more of a nuisance issue. He simply didn't want his double-agent cover blown by an associate insider with proof, so murdering Geronimo was killing two birds with one tire iron.
As to why Brenner is engaging in this behavior that's put him in position where he feels he must kill Geronimo, the key is when Columbo visits his home and sees he has everything. Brenner then dismissively says, "I find it dull." Clearly, Brenner has been doing all this extracurricular work of double-dealing etc. because he simply wants to look for more thrills in his life as he sees it.
Don't forget that this was 1975, so that $350K would have been more than $1.5 Million in today's dollars. Not exactly a drop in the bucket, even to someone of Brenner's wealth. But yeah, it's also clear that Brenner simply wasn't too keen on Geronimo turning up alive.
This is a great episode. PM's acting is fantastic as is PF's.
I imagine Brenner kills him for the money and for the blackmail. Brenner obviously knows something about his victim - that the victim WIll definitely turn on him. The victim underestimates Brenner and is not aware that Brenner will kill him.