Yes, it's much easier to apply rules to an interface especially if the clients you're trying to filter are using DHCP and hence may change IP address. This also offers real separation between the two internal networks, much better security. If you're adding further networks you may want that on a futher separate interface. You can always add rules to allow the network to talk to one another but you can't segregate them later if they're all the same network segment.
I have no idea what sort of distances you're operating over here but often in this sort of situation using VLANs and appropriate managed switches can makes things easier or at least allow you to do things with only the existing cabling that wouldn't otherwise be possible.
Normally I would suggest getting brave and trying one of your routers with OpenWRT and using that for VLANs but neither of yours appears compatible. :(
DHCP should not be a problem since devices behind pfSense will only see the pfSense DHCP servers. Only the pfSense WAN interface will see the Microtik DHCP server.
Keeping things simple is key for an easy life here, minimise the number of devices you have. What will the Microtik router actually be doing in this setup?
Steve