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You're giving both of them too much credit.
Zod et al may not have the experience of using Kryptonian powers like Supes has, but they still have the strength.
It's doubtful whehter Mags could pin Supes in place on his own, let alone three people of similar strength.
I think Zod and co would murder them all.
Wait, Marvel Boy, the Quasar clone complete with his own set of Q-bands? Team Marvel wins. His bubbles were strong enough to hold Herc and the Avengers. The only way they "won" was when Vision phased through the bubble and threatened to solidify inside MB's chest if he didn't free the rest of the Avengers.
Magneto's shields were strong enough to withstand a pounding by Thor with Mjolnir and She Hulk.
If the two of them bubble up the Kryptonians, they ain't getting out easily, if at all. If anyone on Team Marvel figures out the red sun thing, the Kryptonians die. Marvel Boy has complete control over the EM Spectrum of energies thanks to his Q-bands and Captain Marvel can turn into any energy in the EM Spectrum. Either of them can bring forth red sun radiation and destroy Team Krypton.
Mags + Cap Marvel + Marvel Boy win it for Team Marvel.