Priming the beer would be your biggest problem if you bottle right from the secondary, I wouldn't be too concerned about stirring up some yeast. I would advise against adding granulated or corn sugar directly to the bottles, but prime tabs or some form of sugar tablets could work... I tried prime tabs once (one tab per bottle) and I had alot of gushers and the beer had a cidery taste, so I couldn't in good conscience advise those either.
Instead I would say just bulk prime your beer, it works great and isn't all that much extra work.
Primary: Empty :(
Secondary: (I don't believe in secondaries)
Keg #1: The Pilsen Ale!
Keg #2: Sherwood Brewing Co. Irish Stout
On Deck: American Brown