The house of worship went up in flames last week.
L&I discovered more than a dozen adults living in the rectory, in what they call deplorable and unsafe conditions.
They have issued an intent to cease order and will close the building with the exception of two church offices on Monday.
L&I also said it is monitoring plans to demolish the roof, and will intervene if necessary.
A massive fire broke out at the church last Tuesday, shortly after workers used a torch on the roof.