Dororo in Keroro Gunso uses 'de gozaru' too. And Keroro uses 'de arimasu,' and Tamama ends every sentence with 'desu' even when it's not necessary. The weeaboo route of transcribing directly is completely ridiculous, especially when considering that the audience aren't Japanese speakers and will only be thrown further out of the narrative by random inclusion of nonsensical syllables. It makes all of the dialogue doubly unnatural, and it makes the characters who use these endings sound like retards.
Of course, since these phrases all have the same meaning-- and of all things, it's an untranslatable copula to begin with-- there's no way to directly represent them in English, and it's pointless to try. The best way to deal with a character who uses unconventional endings is simply to translate their dialogue in a way that reflects the fact that they have an unusual way of speaking. In Kenshin's case, 'de gozaru' is archaic and semi-formal, so just writing all his lines so that they're just a little bit more old-fashioned and polite than other characters' is the way to go. It's closer to the original meaning in the sense of how it comes across to other characters, and you don't have to throw in anything weird that makes the reader (or watcher) stop and wonder why the hell he talks like a faggot.
I would argue, however, that at least attempting to render it in English (with a phrase like "that it is") is superior to leaving in Japanese words.