Yes. the minutes silence does not frm part of the match protocol, but is a voluntary observation.
As such, IMO it is best practice to ask both teams if they wish to observe it before KO, if they beoth want to, and you re happy to conduct proceedings then crack on as normal. If an individual player does not want to then they stand to the side, hopefully in silence.
if on the other hand there was a whole team (or majority of a team) that did not want to participate, I would see that you then ask the team that does, to conduct their own (with or without you) pre match in their dressing room / side of the pitch.
As referees we are there to neutrally officiate a game of football. We can not allow ourselves to be drawn one way or the other in terms of bias on ANY subject matter.
I have had a team that did not want to do the minute - hence me deduction of the above. I am in no position to "force" someone or whole team to do something like this.
To the contrary, what if you had a team that either requested that it NOT be done, or who are / were in obvious support of those against whom the whole day of remembrance is aimed - waht would or could you do then?
Sit on the fence, do your bit how you wish to do yours, and involve those that with to partake also.
After having served my time I knw how I would "like" things to go, but out on the pitch it's a different head.
Just one thing I and pretty sure on - if you have a 1030KO, don't be stopping at 1100Hrs for 2 minutes. You will both confuse the heck out of the players and have to figure out the correct re-start (dropped ball unless meticously timed for a TI . GK etc???)