Sure it will work!
If you can find some filler (colloidal silica, micro-balloons, "fairing filler", talc/baby powder) to give it a "peanut butter" like consistency that will let you mold and hold its shape and really help them look awesome. Otherwise, just put a dam at each end of the fin and let it setup that way. Just be cautious for gaps between your fin and airframe as you may have a little leakage - i think that the BSI 30 minute is pretty thick so a small gap likely wouldn't leak much but if you have a giant gap you might lose a bit of material while the epoxy sets up.
There are many threads on this topic but I think that I used this page when I was figuring out how to do fillets:
https://www.skypirate.net/rocketry/con_fil_01.htm