***Moved to the Philippines regional forum for country-specific advice***
The embassy will have staff who can translate for OP's wife if needed. Given the situation OP has described, his wife should definitely request that the interview be conducted in Filipino.
The Manila embassy does not make a big deal about excellent English skills. School subjects are taught in both English and Filipino, so it's assumed that any Filipino with at least a high school education knows basic English - enough to hold a simple conversation.
I agree with the others that working on communication skills is important not just for the interview, but for the relationship in general.
A little background about Filipino culture for readers who may not be aware: social status in the Philippines is partially measured by how well one speaks English, and many find it deeply humiliating to make mistakes while speaking English, to the point that they will simply say "Yes/OK/Yeah" even if they didn't understand. They don't want to lose face by admitting that they didn't understand what was said.
Many will also take offense if someone points out their English deficiencies. It's akin to telling them they aren't educated enough.
Nevertheless, mature people in a cross-cultural relationship should be able to navigate these language barriers with kindness and cultural awareness on both sides.