https://stackoverflow.com/a/47837940/260805 hints that it should be possible. I would like to disable it for a longer period of times (~2 days) when enabling incremental repairs.
(Disclaimer: I'm a ScyllaDB employee)
As far as I know you can disable autocompaction in the following ways:
$ nodetool <options> disableautocompaction -- <keyspace> <table> ...
(I think this one is supported only in Cassandra, but not in Scylla)