The upgrade offer has no expiration.
RE: Pro renewal – I suggest that you upgrade to Prime since your Pro is up for renewal already (i.e. you have used up the yearly subscription so you aren’t wasting any “unused” time). But you can stay on Pro if you prefer to have transferable licenses and need faster support. And no, you will not be pro-rated when upgrading to Prime.
We gave gmail users a free upgrade as a way for us to apologize for the initial communication snafu. In hindsight, this wasn’t the best approach as you can tell from user complaints (i.e. those who are on Google Apps) but the intent and spirit of our upgrade was always about “customer first”.