Certainly the clicking thing is an issue. I only ever have the opportunity to click on abilities in PvE where everything politely stands still while I kill it. I think I had a "rebind my keys party" twice while I leveled, and now I'm finally pretty happy. I have five spare buttons on my mouse, and I dedicated those to most of my defensive cooldowns and zen/transcendence.
Speaking of, my first targets as a Sentinel after healers are those annoying imperial agents
A couple times I've come up short attacking a sniper type, though I didn't realize force choke breaks cover... that's excellent news! Mostly though, any target I have my mind set on will die, provided I don't get primaried by tons of people and/or a healer comes into the mix (in which case I can try and interrupt them a few times and burst my previous target down, or just switch to the healer). Guarded by the Force really helps with getting swarmed too, it buys those few extra seconds to kill your target before you go down (or better yet, camo out of the area).
Though I will admit I have noticed some of the tendency to primary "two lightsabers" and I try to keep my blades sheathed until I'm actually fighting, heh.
Oh, and since I picked up such a nice tip from you, here's the two things I've noticed fighting agents.
1) Your friends are a liability if they are near you, because I'll use them as a jump point when you're in cover. Mostly noticeable when there's an elevation change between you and me.
2) I'm pretty sure Zealous Leap doesn't care about cover. It's only 10m range, sure, but I've used it to jump between levels in Huttball many a time when Force Leap was still on cooldown (after getting knocked off yet again hehe). Can typically counter this by staying further back from the edge.