The advantage of using an ORM is that you can always not use it in the places where you are doing things that are not suited to the strength of the ORM.

I tend to hand-write almost all of my migrations and many of my queries that synthesis data from multiple tables to reach a conclusion. I can think of only a handful of times where it was worth writing custom code to persist state (usually only when there are a large number of records that need a couple of specific fields updated.)

Like many tools, it all depends on how well it is used and how well it fits its use-case.