Yes, you need to upgrade your factional MIC to receive the benefit of the Polybian reforms, and if you leave it as is you will still be able to build Camillan units from that MIC. If you are at MIC 5 already, you will need to rebuild that 5th level. If you are at a lower level, you will upgrade to the next highest. As a player you can choose to leave these buildings at Camillan throughout the Polybian era, but that's certainly more a gameplay decision than a historical approach. (You certainly aren't required to upgrade immediately; it's up to you when you do so.)

The Marian reforms are fundamentally different. Once they come into play you will no longer be able to build Polybian units (or Camillan, if you never upgraded). The Marian MICs will be dropped by script into the cities with Camillan or Polybian factional MICs, which you can then destroy for cash.