This was a bad veto for the reasons already given. In this case you yourself admitted it wasn't collusion, but you have asked for a procedure that will 'prove' collusion. You should rather attempt to populate the league solely with trustworthy people and then let them manage their teams. I don't really have any anxiety about how I would prove collusion in my league.
It would be redundant to explain again why this was a bad veto but let me make a few other comments.
I sent an email to both parties stating that this trade was uneven and to rework the deal to make it more balanced and I would approve it. i.e. team 1 include one more non injured player, or team 2 remove Welker.
This is way too much micromanaging. Don't take this the wrong way but from my perspective you are just abusing your commissioner powers. You're lording veto power over them and telling them "remove Welker / add Grossman / etc". That's bad form, commish, and is guaranteed to create more future problems. You are not the oracle of perfect trade equity. Just veto it or leave it.
There are some things I handled inappropriately mainly I should have contacted both parties before I vetoed the trade to see if they would rework the deal before bringing it to light to the whole league. In the future I will do that, though I don't suspect this will be an issue again.
What do you mean by "bringing it to light of the whole league"? Does 'it' mean the trade itself, or your veto? Has the league not even seen the accepted trade yet? If not, there is a huge problem with what you are doing. I hope that's not what you mean.
But even if the whole league has already seen the trade, again, proposing reworkings of deals is just meddling, especially if some information is being hidden from the rest of the league. Stay out of it.
Keeping your veto threat private from the rest of the league until after you try to engineer some backroom coercion on the involved teams is also awful. Everything should be transparent.
The closer to the trade deadline the scrutiny of trades increases.
This makes no sense to me. The trade deadline's purpose is to prevent a certain set of problems. But now you want to use your intuition and judgment to prevent those problems before the trade deadline? No. The trade deadline is when you no longer allow trading. You're saying the trade policies are dynamic and continuously changing up until the deadline. No good.
My suggestion is to be more open minded about keeper league trade strategy and be far less quick to use your commissioner powers, both in your vetoes and in your behind the scenes dealings. There's no reason at all for a commissioner to be giving trade reworking advice, especially if the rest of the league is in the dark about the trade or the veto. That's an obvious source of many future problems. I'm not surprised there is a rift in your league now.
It creates a major situation in the balance of the league, the consolation bracket gets significantly weaker with the top player giving his team away, and the money bracket gets significantly weaker by allowing one team to totally change his lineup by giving up a couple benchers, and a great tight end. So what should every other manager do? If that trade goes through the only thing they can do is try the same type of trades.
People who like this kind of stuff create keeper leagues. I'm confused why you created a keeper league. Keeper leagues, just like major league baseball and some other leagues, create a system in which contenders trade for the present and bad teams trade for the future.
You keep harping on "these teams are in contention" and "these teams are out of contention," which means the above poster is right---you are being short sighted. Every single team is in contention. For the future. If you don't want transactions based in the difference between contending now and contending in the future you should play redraft or have an extremely early trade deadline. But really, I doubt the trade deadline will stop your concerns. You're probably then going to worry about teams out of contention making waiver moves for the future, dropping "studs" and screwing things up among those who are "in contention."
Your job is to create a fair set of bylaws, not to tinker throughout the season in search of "balance." Only an oracle could see the future and provide balance. I think you are imagining problems and making your role as commish way too active. Good luck!