We've wanted to make this change for the last 18 months, but needed our Enterprise business to be big enough to enable the free use of GitHub by the rest of the world. I'm happy to say that it's grown dramatically in the last year, and so we're able to make GitHub free for teams that don't need Enterprise features.
We also retained our Team pricing plan for people who need email support (and a couple of other features like code owners).
In general we think that every developer on earth should be able to use GitHub for their work, and so it is great to remove price as a barrier.
If you as a SaaS provider outsource your SAML integration to a third party provider like Okta or Auth0, the auth provider pricing is immediately on a "call us" tier, with a per-federation pricing in the low four figures for each company connecting via SAML. Let me just state that again, to have company X connect to my SaaS via SAML, I as the SaaS provider have to pay my auth provider $X,000 per year for the privilege, not counting the base enterprise tier pricing for the auth.
Instead of directly bolting SAML into your app, I think a FOSS implementation of an independently running service is the way to go. You run the battle tested open source service (locally / in your cloud), it accepts the SAML assertions and mints something sane like JWTs which can easily be consumed by the service providers, isolating the entire thing from your core app and allowing it be used with any stack. E.g. essentially an open source locally deployed Okta. Doesn't even need to do any user management, just focus on rock solid interoperability and forward all decision making to the actual app server.
The opposite certainly exists though, for example simplesamlphp which gets commingled into a php app codebase as you described.