In Europa league you can play you b team until the latter knockout stage, not so for CL, most games are competitive even in group stage.
You can rotate to a certain point like, but I don't think you can just throw the B team out. Whenever I've watched United in the Europa League this year they seem to have had about 70% of the first team squad out. I don't think the Champions League would hamper them any more than the Europa because I can't see them staying in it past the last 16 - first half decent team they draw I think they're going out over two legs.
Whereas the Europa League is something they can have a go at, plus you go into a last 32 in the knockouts as opposed to a last 16 like the CL, meaning you've got to play a potential 8 knockout matches before you reach the final as opposed to 6 if you were in the CL (not like they would get anywhere close to a CL final like!)
They're very lucky in a way that the season has ended the way it has, with the Europa League knockouts being played after the domestic campaign has finished, as I'm sure it would have hampered with their league form towards the business end