It IS annoying but honestly it doesn't have much of a impact on the whole. I mean while you're leveling nearly every planet has one you can buy. As far as level capped content he is only used for dailys and/or gathering runs. Not to mention the fact that if you must have a moldable weapon now...there are quite a few other companions to chose from.
That, and I retired Qyzen the second I got Tharan. Just jockey aggro with him and you're fine.
Healing specced sages have pretty decent dps anyways, I'm sure it takes me longer than a pure dps class to kill stuff (especially a gunner lol) but I don't really find myself roiling in frustration over my kill speed, and I pretty much can't die if I watch my pulls. (Which is a big 'if'. I still do die all the time, but it's always my fault when it happens.)