Yep. It's possible to cut them in place, but I would mark them just below the top of the body/bedrail, then pull them off and cut them in a vise or clamp. Sawzall probably won't work well. Nor would a jigsaw because the metal is tough AND flexible. If held tight enough though, they might work.
A grinder would do the trick for sure.
Now that I think about it some though, I believe we cut all of ours off with simple hacksaws. Of course, we'd never seen a hand held angle grinder and only dreamed of having a reciprocating saw like a Sawzall! Hah, those were the days.
Heck, maybe you could integrate them into some sort of blocking cap for the stake pocket holes in the corner? With the soft top that hole is open to the outside and will suck the dust into the cabin, as well as exhaust fumes.
Closing off those holes is a big bonus with a soft top.
Paul