While you can, I don't recommend that you should. If the service has been set as dependant on SQL Server, there's probably a good reason. Removing that dependency may cause unexpected behaviour. At least speak to the vendor before you go and change the configuration of their app's services.
Gail Shaw
Microsoft Certified Master: SQL Server, MVP, M.Sc (Comp Sci)
SQL In The Wild: Discussions on DB performance with occasional diversions into recoverability