The point is it stops being an "Ottawa" team. It becomes a Montreal team. Even worse, it becomes a Montreal team controlled out of Montreal. Suddenly we're losing our best players before the playoffs and having young untested guys forced into minutes to get playing time the parent club demands. The point of a farm team isn't to win games, it's to develop players for another club elsewhere. Noone will give a damn if a farm team Fury goes 0-11 if they develop one superstar Impact player.
Sorry but if you don't understand why independence is important in soccer, then you don't understand soccer. B teams, reserve teams etc... are not considered fun to watch outside North America (and even there they're always treated as an inferior product no matter what). The Premier League has a completely separate reserve league for a reason, and they don't pretend to be anything but a reserve league by basing the teams in other cities and calling them unique names.
Sure the NASL/USL/CPL aren't top quality, but the independence means what the team wins is for Ottawa. We get the glory. Which is the whole point of following pro sports isn't it? Plus being independent opens up a whole realm of possibilities in soccer not available in other sports: Canada Cup tournament, international friendlies, CONCACAF etc...
Anyways, it looks like this all might just end up being a harmless 'affiliation' (a few loans here and there) instead of an outright farm club, so I'll put down the pitch fork for now.