Welding down the engine cover so nobody can get to it is however a step too far in the other direction.
Obfuscating is equivalent to welding down the cover... It's actively trying to avoid anyone even looking into the engine.
The worst case scenarios given seem rather exaggerated. When looking at the addon download counts, 3rd party plugins aren't used THAT broadly. That 3rd party addons break at some point is to be expected, using documented or undocumented features, and i'm sure the majority of users understands that from the get go. While teachers can teach their students the principle very easily. But this issue of users misunderstanding what a 3rd party addon truly is and how it's supported could be further mitigated (actively and passively) through multiple ways by Scirra (as suggested already).
So even if you've been burned before or learned your lesson, why go into the extreme?!
I can't wrap my head around how possibly breaking 3rd party addons or projects every once in a while (which can be fixed by the community/users) can be compared to such an extreme counter-measurement. Which obviously does much more damage to the product than breaking all 3rd party addons altogether could ever do.
We're all aware of the warning and its consequences, and everyone is entirely happy to comply with that as much as possible. If there were feasible alternative workarounds, we would have done it in the first place, it's not like we've been given a choice.
Personally i would love to see Construct deprecating things (and breaking old projects) much more in exchange for greater enhancements. Or at least replacing certain features in a similar fashion to what you've done with the new functions. But i understand why you're trying to avoid just that.
Either way, appreciate the open conversation here.
Let's hope for the best.