Sure they needed to.
If the point of all of it was for the mutant gene to be restored, that meant the Phoenix going to Hope. The P5 never surrendered the power to her, and according to Wanda none of them were strong enough to. The only option as far as any of them knew was to beat the Phoenix out of them. And it worked... freed the P5 from the Phoenix, and allowd Hope to restore the mutant gene.
"That's a very nice school you have here, it'd be a shame if someone dropped some Sentinels on it"
There is the possibility that from the Avengers beating the PF out of them, they actually saved their lives. As we've seen in the past, those who aren't strong enough mutants to host the Phoenix burn out from having it for too long. The post-AvX stories have shown us that (aside from Magneto who it needs to be explained due to him not having it), the P5 have had their powers messed up from their time with the Phoenix. Had the Phoenix not been forced out of them, the end result could have been worse.
Holding out for a Peter/Miles team up.
The X-Men got beat up and then thrown in jail, that doesn't seem much like winning to me. The real winner in this whole thing is of course Wanda, who stepped out from limbo to reclaim her rightful place as leading lady of the Avengers, and by extension, the entire Marvel universe.
Also towards the end the Phoenix force would probably have gone through with incinerating the planet, which was the fate of all the other planets on its path as it approached. So somewhat unwittingly the Avengers bought enough time to forestall the ultimate destruction of the Earth.
"...Doom's enemies have not the mettle to challenge him host to host, tooth to nail... As economic and military options fail them, they resort to simple rudeness."
Cyclops flat out tells her to her face that she doesn't deserve the Phoenix. And we're told in issue 12 that no one except Hope has the strength to let it go.
In order for things to get fixed, Hope had to get out of Utopia and help from the Avengers. That's what needed to happen, and that's what happened.
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