I don't think it's that tough of a position for the DOJ. I think for far too long the DOJ has just acted as part of the executive and often makes decisions in line with "what gives the executive branch... the president... the most amount of power?"
If there is a serious risk of civil war, that's why the US has it's national guard part of the military - isn't it? Part of the biggest issue with January 6th is while there was plenty of evidence of the risk of what happened, it seemed like there wasn't really adequate planning in the face of that known risk.
At this point with January 6th they don't just have evidence against the political figures that played their part in coordinating what happened, they've got evidence against leaders of these militia groups - charge and arrest them in conjunction with any political figures implicated in January 6th & have the appropriate officials in every state ready to respond to potential threats of violence from these militias.
These people are still a fringe minority and many people would be less likely to join people like this if they know there will be serious consequences to their actions.
I think it's a much tougher decision for the DOJ to not prosecute. It shows that people connected with the rich and powerful can get away with anything, even attempts to overturn elections. I think for a lot of the country, it would just underscore the fact that the justice system in the country is a joke and that the ultra-wealthy and well-connected.
And it should not be a partisan issue. The DOJ holding that a sitting president is within his rights to overturn the will of the voters is an awful precedent to set - regardless of whatever political affiliations anyone might have. It should scare republicans as much as it scares democrats that the department of justice could turn a blind eye to abuses of the president that degrade democracy - because the precedent set isn't one that would just apply to republicans.
Republicans should be wanting the DOJ to do something because theoretically it gives Biden (and any other democrats) carte blanche to do the same thing Trump did. And with the midterm elections coming up, perhaps telling them the DOJ could give Biden the power to try to overturn the results in November might light a fire under their arses to actually look out for their country instead of being afraid of how their voters might feel for a few months.