There are really 2 separate issues. The license count is an easy fix. Since ExpressionEngine went open source with the release of version 5, older downloads are available for free. And if you have MSM installed and need another site added, just drop an email to firstname.lastname@example.org and they’ll help you out.
Second issue- deleting the primary site. That’s less easy. There isn’t a ‘clean’ way to delete the default. I can think of two options- swapping out another site to be the new ‘id 1’ by manually altering all of the site ids. Or possibly hacking it so the delete routine works on id 1. You’d have to be super careful with either option.
Given the choice, I’d leave it and just add another one.
If it were me, I’d delete the entries, channels and templates from the primary site and either re-use it or let it sit. It’s not going to hurt anything to do that and you don’t gain anything from simply switching the site id around in site_id 2. And there are just a lot of places for it to go wrong manually switching it.
It’s definitely not worth the work and the risk to try and make a different site the ‘default’- there’s no benefit to it.