I've been playing around with a few merc builds - Necrolyte, Abjurer and Priestess.
The advantage of a rogue seems to be more in its AI and the build/playstyle being used. I've noticed that a rogue tends to stand behind me whereas an A3 merc (certainly the abjurer anyway) tends to stand in front, where it gets shot easily. Also, as I mentioned above, the necrolyte AI in 2.0 tends to just spam ice nova out of range, which is a waste of effort.
Also, in terms of playstyle, by casting hydras ahead and into doorways - and keeping 10 scourges up - I reduce the number of times a rogue is in danger. They tend to be most useful when something gets near, and they slow it - I'm basically keeping it alive just to do that.
With any merc, the most dangerous time is when I first enter a lab - if lots of stuff shoots at us that could be the end of the merc (or me). Also, using teleport defensively helps, not just to defend my character's life but the merc's as well.
And I use the innate paladin skill a lot as well, to give life regen to the party for 30 secs.
The gear I have found best so far has been either the set + witchunter's hood + endless loop and I only have Angel Heart ammy. Or using Askarbyd in a similar setup but with a Rogue rw in Ancient Armour for defence. I'm still trying combinations based on what gear I have.
I'm about to try replacing Amethysts in gear with more Um runes to up her effective resistance. My own stacked resists are around 280-290 whereas the merc doesn't have anything like that - it's probably its major weakness especially with T9-10 mobs having an extra -100% pierce.
TL;DR The holy caster build and a careful playstyle has ways to help a merc stay alive: ranged play, hydra turret, 3s teleport, 10 summons, innate regen skill for party etc.
When I said it was "better", I meant just that - not necessarily "good".