The trouble is currently focused in Minrathous, so the borders beyond the city won’t be closed and your characters can return to Kirkwall without incident. There are smaller numbers of pro-Venatori types throughout Tevinter, so if you want characters to run into someone who tries to stop them from leaving the country because they appear to be with the Inquisition, you can do that! But it's very optional and would be bad luck and running into the wrong person, rather than any sort of concerted effort to catch them or other large-scale enemy activity.