I notice that in the latest version (4.2) of the Windows Service Console there is an option under 'Advanced' to 'Show active server actions'. I haven't played with this, but it looks like you have the ability to kill an action
We used a java-action to kill specific scheduled events/microflows.
Create an entity (called control or something) with a boolean attribute and create a button to change the attribute. At the start of the MF you want to stop during run time, retrieve the first control object and do a false/true check at the start of the MF and place this check at the relevant places in your loop with a break event.
For example if you set the attribute to false while the MF was busy looping, the split will now go the break point and end the MF.