No I don't think the Red Alerts should be restricted at all. From a story perpective when Starfleet hears that there's a crapton of borg cubes invading alpha quadrent they are NOT gonna be choosy on who can come help stop the borg menace (A similar invasion is what allowed all of our respective captains to acquire our first ships remember?).
From a metagame perpective teamwork issues are prevalent through any MMO or raid action and as one of those low level players in those red alerts I know that i'm focusing on the probes not because im "farming" but because that's the only thing it appears that I can damage without help in those events and hopefully still be useful while the RA/VA big boys deal with the cubes and the command ship.
see but you should just be focusing on victory and not on the probes, I have lost many instance because lower level players probed farmed or thought they couldnt do it, only be working together and following the team leaders orders this is best way to obtain victory have confidence in yourself if you think you will loose you will loose