We are putting a process in place where all architecture changes must be documented.
Are there any standard templates for documenting alternatives and decisions?
Depends on how detailed / formal you want to be. In terms of a Decisions Register we'd normally use one doc per area / decision, although recently we've been experimenting with OneNote.
At the very least you want to record (for each option):
A succinct bullet-point list of pros & cons (etc) is usually sufficient - it doesn't need to be a big doc.
For a more in-depth / formal / complex scenario you'd want to go further, this is the format we were using in such cases:
Summary
Evaluation Criteria
(This is important as it sets out the criteria you used to score the available options, including weightings etc).
Summary of Recommendations
[Option 1…N]
Recommendation