That's what we do, and did with Atomic. We all learned the full-length version but after we'd been through it a few times, we all agreed it was too long and meandering to play live. We couldn't nail an arrangement we all liked - the closest we came was to heavily prune the lead into and out of the bass solo, and finish on a shortened verse with the final 'Atomic' sung a capella. But we had gigs coming up and half-a-dozen other songs to learn for them, so we just let it go. I've suggested reviving it a couple of times, but no-one seems that keen.
As an aside, Atomic's not the only Blondie song guilty of going on too long - when we did Heart of Glass, we decided to go with the Miley Cyrus arrangement as that felt much tighter. It goes down well.