In addition since the Scottish referendum there have been two elections, one Westminster, one Holyrood where we have had the majority of votes for parties against leaving the EU and committed to oposing it. In the Holyrood manifesto a specific commitment to a further Indyref if there was a significant change in circumstances ), i.e. Brexit. And a 62 -38 majority in Scotland in the referendum against Brexit.
Further, the initial position of the Scottish govt was to look to work together if they felt that there was a way to do in line with Scotland's interests. Now it may be that the UK govt felt there were certain aspects of the proposal that were problematic but negotitiable but they didn't make that case and appeared uninterested in doing so. Combined with the collapse of the Labour party into a morass of soft coups, and the rump of the Lib Dems being in no position to be any real break, then it looks like Tories for the next 20 years unless things go humungously tits up because of Brexit. And since that is what you are seeking to avoid, the combined factors make this inevitable even if the timing might be questioned.
As a speculation, i wonder if the timing might have been influenced by discussions with EU reps, particularly Verhofstadt