Yes, I think the federal government should be able to use force in order to quell a rising millitia force. I think that rising, fringe militia forces that are uprising can pose serious threats to the government, and when they are provoked it is time for the government to use their own force.
The government should use force to quell a militia movement if the militias movement turns violent and starts to disrupt day to day life. Now, if the people as a whole are behind a militia movement, the us government should listen up and begin to change things and meet demands.
The US federal government should not involve itself against militia movements that represent no immediate threat or cause any risk. Especially if talking about foreign areas, these militias impact the US interests very little, but this would involve us in too much conflict. If domestic, organizing a militia is a given right and it would be absolutely wrong for the government to intervene.
The use of force may pause the militia movement temporarily, however it does not quell the beliefs and values that lie underneath the movement. Using force to quell a militia movement may only create violence and political confusion. It should be up to the people and politicians of that region who decide how to deal with a militia movement.
If the government truly wants to prove to it's citizens that it is not a borderline evil fascistic state, it would be in it's best interest to not act like one. Proving the point of many militia movements (that the government is oppressive) should be the last think the government should want to do. Furthermore the idea of a government, any government using force on free citizens who have done nothing but exercise their first and second amendment rights, will not further their cause of wanting to be seen in a positive light.
The day a government takes up arms against it's citizens is the day it takes a major step towards totalitarianism. If the government did this they would be proving the militia movement right.