I always decide based on the character I'm playing. If my charcter hates the BOS then, well, you can see she might just go with
Spoiler blowing the Citadel into a smoking crater and shooting Sarah Lyons in the back.
That can be a lot of fun. However, if my character has been hating the Enclave the entire time and enjoying the BOS and thinks they are great, then doing it would make no sense to me. It certainly isn't worth doing for the stuff you can collect.
The above is only my opinion. Make a save at the point right before you make your decision. Play it out and if you don't like the consequences, reload and choose the other target.
And, like Ghouls says, saving beforehand is always a good idea in case you hate the decision you end up making. Then you can always go back and do it the other way.