I'd say V's still on the cusp of neutral, but only just barely. Kubota was just as dangerous bound and captive as he was running free, or just about. He would have tied the group up in complicated legal proceedings for an indeterminate amount of time (they've already experienced the Azure City Justice System firsthand, and V knew what he'd be in for), which would keep them from their Epic Goal. Not for nothing, Kubota would be in his element in such a trial, and would very likely have gotten away with his crimes. Which he had confessed to.
It's a thin justification. He freely admitted his evil deeds, and was in the process of spelling out how he intended to get away with it, but V didn't Dustpan him for that...he Dustpanned him because he was an inconvenience.
V's teetering on the edge of the Slippery Slope. S/he needs Roy around to keep him/her grounded.