oh god no. you'll break everything. SMGR's web apps to SMGR's db are cert protected. SM's mgmt interface to SMGR too. all down the line you'll make life hell.
You can make SMGR a sub-CA of MS and re-enroll everything. That way everything would chain up to the head-end MS CA anyway.
Or, you can put specific MS certs on the interfaces that'll talk to your clients - like the SM interfaces, or the Presence Server, etc.
Depending how much stuff you got - AADS/AMM/PS/SM/SBC/etc/etc/etc, doing it the 'Avaya way' with SMGR first might be best. That doesn't preclude you from using SMGR as a sub-CA to MS and still having everything chain up to SMGR. Just depends how much of your hair you wanna pull out.