I racked too early

I could have sworn the beer was ready to rack, so I stuck the siphon in the airlock hole and racked away. In hindsight that was a bad idea.
Anyway I got enough yeast carryover and there is def. a good fermentation going on in my secondary.
I was fermenting a lager so I underestimated the fermentation times.
Can I let it finish fermenting, give it a couple of weeks and transfer to a keg for lagering?
How might this affect the flavor?

If it's still fermenting after you transferred it, I'd wait until all visible signs of fermentation have stopped. I don't keg but I would imagine that once fermentation as stopped that you could rack it to a keg and begin lagering.

The tail end of a lager ferment can drag out for weeks. Let it finish and verify it by checking the gravity. Then keg & lager.