In some ways, the “best” way to handle this kind of thing, especially if you want it always set for all users, even future users, is to use Local GPO deployed with BigFix to delete this.
A different option is to use relevance to get ALL of the user keys that have the unwanted value, then actually delete ALL of them using a BAT file or similar.
The other option, which is the one you are covering here, is to delete the value but only if a user is currently logged in that has that value, and only from that particular user.
The option in which you are deleting the value from only the currently logged in user is bad to put in a baseline for a few reasons. One is if a new user logs in with the value, then it will run again. The other is if the current user checks the box to set skype to start with windows themselves, then it will run again. The other is if the software itself puts the key back, then it will run again.
This kind of configuration is better done as it’s own action all by itself.
That said, if your actual goal is to prevent it from starting with windows for all users regardless of user preference. Then I would recommend the Local GPO option.