You buy a camera to use it, so why not use it. What's the worst case scenario? The shutter mech dies... At which point you have 2 options, get a new body or fix what you've got.
You don't especially need the latest/greatest DSLR for timelapses so long as you have a decent lens you could probably pick something cheaply second hand and use that until it dies. Something with a half-decent sensor that you can hook an intervalometer up to will do you.
Or you can get it repaired when it dies... That's not likely to be hugely expensive, even if it's $250 it's not the end of the world for something you use every weekend.
But... If you're happy to shoot video (then video production SE may be better to ask) as an alternative to framegrabbing odd frames you'd be better off averaging groups of frames. I suspect you'd get quite an interesting (possibly smoother) effect that way, or even if you went a step further and overlapped the frame grabs, so pulling frames 1-50 into 1, 25-75 etc.