Let me get this straight, today you have 2 physical switches each is a separate fabric, they do not talk to eachother. You are moving to a single 9506 director. The current switches do not use VSAN's, but you are asking if you can create VSAN 10 and 20 on the director.
Yes, this is fine. You should create VSAN 10 and 20 on the director. Connect fabric 1 to VSAN 10. You should use an E-port and disable trunking protocol like you suggested. You can do the same with fabric 2 and VSAN 20. Then copy over all the zones and move the stuff over one port at a time if you like.
There is no issue with what you are discussing. Keep in mind normal fabric "rules" apply, such as timers matching, and other parameters to avoid an isolation. Good luck!
Brian