The email you received wasn't a notice-after-the-fact of a deletion. It was a heads up to let you know there is a related, more-successful proposal you may wish to support. The disparate, education-related proposals are not gaining traction because support is spread to thin, so combining forces into a larger, more-comprehensive site is a useful tactic to getting those subjects launched.
As for sending deletion notices before cleaning out abandoned proposals — No, I don't see the value in artificially rousting support for a proposal that has had ABSOLUTELY NO ACTIVITY for 1-2 months; no new questions, no comments, no voting, nothing.
Getting a site started and making it successful in the long term takes a lot of work and dedicated attention. If we geared this system to constantly prod people "please, please continue to pay attention to this struggling proposal", that is not likely to create a very promising site.
It's not a judgement call on whether a proposal was a good idea. Sometimes you simply do not have the right people with the right knowledge in the right place at the right time; so the momentum simply is not there to create a successful site. And sometimes the process falls apart when it should fall apart, as was the case here of splintering support across niche educational interests at the expense of a much more comprehensive, stronger site.