You're making the common assumption that such a situation would be "the standing US military roughly as it exists now" vs "rebel citizens with only small arms". This scenario is unlikely to ever happen.
What would be more likely to happen is something like the Civil War where the army itself was also divided. Even more importantly, it is a lot harder to control an army when the targets are the people the army supposedly exists to protect. In a survey[1] of "300 U.S. Marine Corps soldiers" about unit cohesion when working with the UN, the final question asked:
46. The U.S. government declares a ban on the possession, sale,
transportation, and transfer of all non-sporting firearms. A thirty
(30) day amnesty period is permitted for these firearms to be
turned over to the local authorities. A the end of this period, a
number of citizen groups refuse to turn over their firearms.
Consider the following statement:
I would fire upon U.S. citizens who refuse or resist confiscation of
firearms banned by the U.S. government.
(__) (__) (__) (__) (__)
Strongly disagree Disagree Agree Strongly agree No opinion
The results of that question suggests a "citizens vs army" scenario is very unlikely.
The results [...] with 88.0 percent responding,
revealed that 61.66 percent said they would refuse to fire on U.S. citizens,
whereas 26.34 percent indicated they would fire. This particular question,
unlike the others, elicited form 15.97 percent of the respondents with an
opinion, either heavier pen or pencil marks on their response or written
comments in the margin space. [...] The responses to this scenario
suggests that a complete unit breakdown could occur in a unit tasked to
execute this mission.
Small groups of people often have some kind of consistency across the group, because the definition of the group self-selects for something. (e.g. the people who choose to attend a chess club tend to like to play chess) As a group grows in size, the makeup of the group tends to become more heterogeneous. Eventually, as the group becomes very large, the makeup of the group tends to resemble the makeup of the general population.
The military is a very large group of people, so the individual attitudes and politics of a soldier tends to resemble the attitudes and politics seen in the country in general. When considering a topic that is obviously politically controversial, you should expect that the people serving in the armed forces will be approximately as divided as the rest of the citizens.
[1] http://www.dtic.mil/dtic/tr/fulltext/u2/a293790.pdf