I would have to see it for myself to be sure, but what you describe sounds problematic for sure. Some easy fixes could include reduced range, reduced damage, reduced chance for KD, higher cost for ammo and so on. I'm sure there's a balance to be found.
But like I said, I want to see it for myself too, and I'm not convinced there aren't any good counter strategy to mass milkor. It might also not be a bad thing to have a hard counter to camping inside tiny rooms with your whole group. I'd rather see both attacking and defending teams be more creative with positioning and flanking. Sometimes it just takes a while before people think of a good counter to some strategies.
As for melees being useless in ZC, I disagree. The point is that you don't have to be melee 100% of the time, just like you can easily switch the milkor to something else if the situation requires it. Melees are excellent in close quarters, and I've seen plenty of ZC take place in very close quarters already. You can also make great use of super knockbacks for example to push enemies into your own lines, it can be really effective. But of course it's all situational, you can't just rush alone with your sledge into the enemy lines, you have to be clever about it. Definitely don't think melees require a buff any time soon. We do need something to replace AC though, some ideas are in progress that we'll try out shortly.