well, you are talking about a possible bias, but don't forget that in this situation you may also be the 'home' ref. Personally I wouldn't go there.
it's easy and trouble free to overrule a TJ who keeps his flag down, you blow your whistle.
it's much more problematic to try an overrule a TJ who puts flag up. I know you will all say players must play to whistle, but I have sympathy with players who treat the flag as a whistle, especially when the players are kids and the TJ is one of the coaching team.
also how do you overrule - a cry of 'play on' is problematic, some may hear you some may not. It's quite random and not necessarily fair.
unless the TJ is demonstrably, clearly wrong I'd go with it.
If the TJ really is flagging for a non-event think it might often be better to treat a TJ wrongly flagging as an extraneous incident like a dog on the pitch and stop play and resume with a scrum (and change the TJ!)