I think your premise that the problem is negation is incorrect. Likewise that there is some precise standard grammatical solution to the problem that does exist.
The problem is that could is used as both a past tense and a polite way of expressing a request or an injunction, and thus — depending on the following verb — ambiguity can often arise if the context is not clear.
To take your example, without the negation, Could you go there? can mean
Were you able to go there?
I wish you to go there.
This does not happen with all verbs, e.g.
Could you see the house?
…is a question about the past, (English requires look at in the imperative form), whereas
Could you see to the children?
…is 95% certain to be a request in the present or future.
Such ambiguities are common in language and rely on context (e.g. tomorrow, yesterday) for clarification in the written language. In the spoken language tone of voice indicates whether something is a question or a request/injunction.
For this reason, in the context of an online exchange, I would use an exclamation mark to distinguish a request from a question. (I think exclamation marks are over used, but this is a simple ‘fix’.):
Could you not go there? (question)
Could you not go there! (injunction)
This, I think, provides a way of solving the problem without altering the sentence. However, in practice, as @Pam and I indicated, the addition of “Please” to the request would put the situation beyond doubt.
Please could you not go there?
and, perhaps also change could to would, which is still technically ambiguous (habitude) but less so:
Please would you not go there?
It would also remove any ‘guilt’ you may feel at omitting the question mark from what ostensibly is a question. Punctuation is not a form of grammar, however, and I regard it as unnecessary (even foolish) to follow an injunction with a question mark. I imagine this topic has been covered elsewhere.