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.