Should I keep the decoupling capacitor's vias isolated from ground fills?
I suppose it depends on what you want to use the selective fill for. Is it supposed to be just a shielding? Is it going to be large enough to be considered it's own ground plane?

In the former case, I'd guess at 'no', but in the latter case, sure. The truth is that it may not matter anyway, especially if the stitching is done well.

One thing I see that may cause an issue is how close the vias are to the component pads. For some assemblers I suppose this isn't a problem, but the one I use wants to see 10mils (10 thousandths of an inch) between the edge of the pad and the via. This helps with solderability and solder-stealing issues.

If you're really stressing about the EMI, you might consider using X2Y capacitors for bypassing, making sure to follow their layout guidelines (6 vias per component)

http://www.johansondielectrics.com/x2y-products.html