Making the sign of the cross when passing a church is a pious custom but is not required of Catholics. The intention behind the gesture is to show reverence for the Blessed Sacrament that is in the church.
Based on the intention of this pious custom it would not seem to make much sense to make the sign of the cross when passing a church that does not have a valid Eucharist. If one wanted to make the sign when passing an Orthodox church, that would be consistent with the meaning behind the gesture. However since its not something that’s required its really up you.
