I've read the Chakuun article on Memory Beta already some while ago and finally got my hands on the EV omnibus earlier this year.
Imho, there's no major continuity reason against including them. After all, the Tholians may have ditched them soon after the 2250s, or they may have suffered a cultural catastrophe - both possible explanations for their absence ever since.
I'm always for a tighter continuity. Comics, screen, novels - I tend to mentally stick them together, with rough patches if necessary. For example, as long as nobody mentions Pike's family history in detail - which is unlikely anyway because Pike's father and the Chakuun have nothing to do with one another except from being from EV - they could be eased into the continuity.