I was thinking of adding all of the pools to default cgminer config and disable them at startup. Bring em up when necessary (enable/increase priority). This should circumvent any add/remove glitches.
I already tried this before but there is a trouble with startum (again!! ;-) pools. When I disable stratum pool, cgminer ignores that pool is disabled at feeds data from disabled stratum and it can be something you don't want because stratum for LTC has different information than stratum for FTC; I use --failover-only switch.