Was first gear revving out and second gear lugging?
I'd just let first gear wind and not really worry about it. I don't think it would cause a problem. I've spent a whole day riding through NYC (not on my Versys) and the speeds were low and the fan came on a lot, but there were no ill affects.
"ride more, worry less"
2005 Suzuki GSXR1000 (slightly bent) - Track
2000 Honda VFR800 - Street