What is the ruling on praying in a mosque where a barrier separates foreign worshippers from Malaysian worshippers, especially given the possibility that the Imam is a Sufi who sometimes makes mistakes in pronouncing letters, and considering that the Malaysian government has prohibited foreigners from praying in mosques to limit the spread of the epidemic?

The prayer in the aforementioned mosque is valid. The separation between you and the worshippers in the main prayer area of the mosque does not matter as long as you can see the Imam or the worshippers. Doubting the Imam as being an innovator has no consequence, for the default assumption about a Muslim is innocence, not accusation. Even if it were confirmed that he is a Sufi, praying behind him is valid and sufficient, unless you know that his innovation reaches the level of disbelief (kufr).