Unfortunately, per-interface rules do not currently function for VTI interfaces. It's a limitation in the underlying OS (either in if_ipsec, pf, or some combination of the two).
Communication from a subnet like that wouldn't necessarily succeed anyhow, though, because your return routing wouldn't send it back to the "wrong" tunnel. In your example, if "Prefix A" came in from "Site-Tunnel 2" the reply traffic would go back to whichever one had the route on it, likely "Site-Tunnel 1".
If you are using a routing protocol (BGP, OSPF) you could filter routes that way as well.