Hi,

I understand what u mean. No it should be ok to not put the supervisor on the referee list in the case that you describe. Do not ever put any referee on your CV who you even have the slightest doubt that he might not give you a good reference. Potential employer will not think of a missing supervisor as a referee if the referees that you have mentioned instead have a good designation and have known you. so make sure the referees that u are using are really good.