Is there anyway to disable engrams in game like you can with the in game server options?

yes it would look something like this . I use this to block a engram so players cant create this item.

OverrideNamedEngramEntries=(EngramClassName="EngramEntrySpyglassPlusC",EngramHidden=True,EngramPointsCost=1,EngramLevelRequirement=10,RemoveEngramPreReq=False)

This blocks the player from creating the spyglassplus in a utilities mod because it has issues.