That's an interesting idea, although I don't think we should confuse it with the Aid Another action, which has clear benefits.
Perhaps something like this?
Demolition (Ex): A builder genie can study a construction to find its weak spots. This requires a full-round action and a Knowledge (Architecture) check against a DC equal to the construction's break DC. If successful, the genie's attacks ignore the first 6 points of the construction's hardness and do full damage.
Instead of making its own attacks, the builder genie may instead use its demolition ability to aid the operator(s) of a siege engine. In this case, the DC increases by 5. If the genie succeeds on its check, the siege engine ingnores the first 6 points of the construction's hardness and deals full damage.