It just takes a WHOLE LOT of practice. Eliters are kind of offensively defensive (which offends some squids! ;) ) You have to defend by being so offensive there's nothing that approaches you to have to defend. Which of course never ACTUALLY happens, but that's the sort of working theory. But either knowing when to retreat or learning how to be evasive and still have a solid chance of winning CQC encounters really helps to not be so team dependent. Enemies WILL rush you and flank you, and they get quite a surprise when they figure out that 2 partial charged eliter shots can still take them out. It's not easy to do, but it can be done. You kind of have to aim like a squiffer, shoot like a bamboozler, all with the mobility of a hydra :p I'm as likely to shoot from the ground at the rear as I am from up on a perch, and in most ranked modes, more likely. Even eliters can help push the objective as a rear-line support, and it's harder for enemies to flank you if they're not actually sure where you're going to be!
If you go up against those S+ Japanese sniper aces, take note of WHERE they seem to be getting you from. I'm amazed sometimes at the places they've thought of to snipe from! After observing a lot of the best snipers play, I've learned to be a lot more aggressive in my use of eliter. It's strange to call it an offensive weapon, but it really can be used that way, and the top snipers do seem to use it that way. Higher tier players know where the sniper perches are and know to go guns plazing at the perches to get rid of a sniper. They're sure surprised when they find the perches empty and still get splatted from across the map by a sniper that was waiting for them. Comparatively the hydra is more "pure defensive" IMO.
I know what you mean about your team NOT paying attention to you getting flanked. That's probably the most frustrating thing as a sniper. And there's little that can be done about it. Ultimately you can fall back and try to take them out until the team figures it out. It won't do much good trying to hold your ground, after all. Let me guess, this happens most on Depot? :D
Oh yeah, the splat charger shotgun FTW! ;) Splat charger's not a sniper rifle, it's the squiffer the way it should have been! ;)