I think you made a good decision there Cubs. In my opinion this was a clear case of collusion initially as stated by Owner A- collusion being defined (in the fantasy baseball connotation, not Amazinz's dictionary definition) of any trade being made for reasons either outside of the fantasy league and/or without the intent of bettering your team/your team's chances of winning.
That said, it isn't a ridiculous trade, and more importantly, I could see the true intentions/thought process of owner A being- "I think Beltran is gonna suck it up. This looks like a deal that would help my team in some positions I need. If I deal Beltran, everyone is gonna say I'm stupid. I don't think this is the best trade, but I'm happy with it- let's find a way to make it fly."
I've found in many leagues that dealing one superstar for another is almost impossible- if you want to move a superstar you have to accept two 2nd-tier superstars as often as not, hence Thome and Foulke, two guys who are first tier guys at their positions, but not first round superstars.
Then he tells you he's doing it cause he feels bad, hoping you let it fly without saying, "haha you're a fool."
Most importantly, it's not a gross violation of no-collusion rules, and a veto could cause decreased league activity, commish-hating, and all sorts of anti-fun backlash. As a commish's job is to keep things as fair and as fun for all involved, letting this slide with a warning was probably the best way to deal with it