A while ago I wrote a little tool to set the time on MikroTik devices. It takes the current time from the local machine and does set it on the device through the API (while respecting the timezone configured on it).
I mostly use it to set the proper time when the device time was completely off (when setting up a new device or when it has been powered off for a long time). Afterwards NTP should take care of keeping the time in sync.

The tool is now available on GitHub together with installation and usage instructions: mt-set-time