Probably not as done as one might think.
For the Malevolence's part, the Ion Cannon is mostly useful for destroying things the Replicators [i]possess[/i] (like warships) but not the little bugs themselves, since they are immune to EMPs. It'll take special tuning to use that against them in the most effective way. And outside that, all they have is brute-force bombardment, which (given the Republic's example) can only go so far against these things.

The bigger worry in my mind is if the Replicators start absorbing Halo tech from the... [i]plentiful[/i] options that this carrier can provide. The Malevolence losing some droids to the Replicators isn't really a problem, since those things are -generally speaking- mass produced trash that won't give the Replicators much of anything they don't already, but Halo tech? That might be... an [i]issue[/i].

In some ways, the weaker the tech you can get away with facing the Replicators with, the better. The less risk you have of them getting their hands on something horribly bad for everyone. Better still, use something that will be useless even if turned back against you. Or even better still, don't face them using [i]tech[/i] at all and use stuff they can't replicate, like any supernatural powers that the PCs hold.