Take this for what its worth, coming from a fella that cut the top off a XJ (Somewhat apples to apples comparison).
I loved having the cut top on the trail, I hated it everywhere else. Unless you spend some good money (or you’re a pretty good seamstress) getting the top to seal is damn near impossible (assuming you do a soft top). With my inability to seal it up decently from the weather, all the interior electronics started to fail within a year.
Physically, after the first few wheeling trips (and few good hits) nothing really seemed to want to line up anymore (doors didn’t like to close, the windshield cracked to hell, etc). Granted, since you’ve got the advantage of body on frame, those issues might not be as bad as the unibody I was working with.
You could allways pick up a Bronco/4Runner. Same idea, but factory built
If this is truly going to be a family hauler/crawler, I’d think long and hard before I whacked the top off. Either way, its your junk, so cut it up (and take pics!). Worst case scenario is that you hate it, and swap another body on that frame.