Hmm, I’m wondering if it’s ever a bad idea to do a command line rebuild. My understanding is, there’s no extra risk. But there is potentially an extra cost: it’s slightly less convenient to do it; with a standard installation it will cause more downtime; and it needs more free disk space to do it. If you’re very short of space, that means more care needed.
In any case, I strongly recommend taking a backup immediately before any upgrade, and downloading that backup for safe keeping. (A snapshot of the machine, if your provider offers you the facility, could also be useful, but it’s not a backup.)