Well, Panzer's the one who should answer all this, mainly, but I'll give it a go myself.
First of all, you have to know that people in the Colonial Republic, in-RP, come from a variety of nations and national heritages. Panzer's president is Greek, for example.
Furthermore, no, it's not that the Colonial people hold grudges that far into the past, except perhaps Panzer's character, I don't know anything precise about that. I'd reckon it was more of a 'looking-for-an-appropriate-insult' to achieve that cold tone which is appropriate in this particular occasion.
As a Colonial, in-RP, I'd tell you that the Emperor was wrong on this occasion, especially because the offending Kusari vessel provoked violence and because the Colonial ships were requested to assist with hostile forces.
I'd also say he was wrong because he acted a bit boastfully and treated an ally like an insignificant little group he can push around and dominate easily. It is not very wise to have a servile attitude in foreign diplomacy, so Angelos didn't really have much choice but to receive the Emperor's criticisms with a humble apology, because that would signify the Colonial Republic as a protectorate and an underling, and not a full-fledged ally, which, when you think about the strong nationalistic tendencies of the Colonial people, as well as their continuous strife in the firm establishment of their own nation whose authority is not disputed.
As an impartial 'guy who plays Freelancer Discovery', I'd tell you that the Colonials should've not went into Kusari at all because they should've thought it all through a bit more and realized what would probably happen, and that they were a bit naive in their actions.
All in all, the smart choice is the apologetic and peaceful one, and the realistic in-RP one is the one which happened.
And no, there's no grudge, at least not OORPly. We lurve teh Zelot.
I hope I cleared it up enough, if there's anything else, feel free to shoot.
<span style="font-familyalatino Linotype">
<span style="color:#000000">All morons hate it when you call them a moron.