Andor is no longer a member, so the Federation can't tell them what to do. Yet at the same time, Andor is in the heart of Federation space, so having a Pact member there would be an unacceptable security risk...
It would probably be like when Cuba aligned itself with the Soviet Union.
The biggest difference would be that the independent-again Andorian Imperial State, unlike the Socialist Republic of Cuba, is a democracy with strong pro-Federation currents in the population. Even with the new disenchantment, these people and many of the anti-Federatino factions would still be opposed to a radical realignment. The ambassador told Bacco that the Andorians weren't interested in cutting off ties with the Federation, just exploring the idea of more pragmatic ties with all.
Presumably there'd be all sorts of overt and covert support for anti-Typhon Pact factions in Andor.