yes. you can leave it there and just unplug the small gauge wires.
personally i omitted the whole circuit on my rewire, including the starter and large positive cables (as there was nothing to really attach them to).
the downside is you pretty much have to rtv the old starter cover down because it bolts to the starter and you have to plug the hole where the drive end of the starter goes into the gearbox. i used an expandable rubber engine block/freeze plug, six years 13,000 miles, no probs.
just means you actually have to keep the bike in good tune or you'll kick your arse straight off trying to get 'er started...