IMO this is simply a matter of colour. My opinion, however, is based on the assumption that Riften is controlled by the Stormcloaks. http://images.wikia.com/elderscrolls/images/3/38/Riften_Guard.png picture shows a Riften Guard and http://elderscrolls.wikia.com/wiki/Whiterun_Guard picture shows a guard from Whiterun. The Riften Guard has blue cloth on his armour while the Guard from Whiterun has yellow cloth. Whiterun is known to be a neutral city and blue is known to be the colour of the Stormcloaks.
If what I think is correct, then the Markarth Incident should be truly a Stormcloak thing, because I read that the perpetrators were wearing blue.



As for the conquering/allied holds thing, I actually never thought of that myself, it would be a nice touch if they added it in.