I'll start from the bottom up...
I'd need to study it a bit in depth to figure out the best strategy for me to integrate when.js in such a scenario.
But this discussion is not about me or how / if i'll cope. It's about the library's future.
In that respect:
1. Is there an actual problem that exists today, that forces you to make that decision?
2. What will be the benefit/s that the library will get from such a decision?
I don't want to touch the namespace subject, as i have strong feelings about it and plan on writing a blog post just iterating on why namespaces are good for you and the community.
My suggestion is that not only you should not drop support for window.when, but augment it with all the helper functions that are now polluting the global namespace.
So window.when_sequence should be window.when.when_sequence (or even better: window.when.sequence).
That would be a change with significant impact to the zen of the library and does not banish vanilla js authors from using the library.