Great Old One
If the PC needed a +7 in persuasion or deception that would come with years of training in a market, maybe I would let the PC swap out some other character things to get it. (Did you give up your school of magic training because you worked in the market place? A point of to hit and your armor training?).
You do realise, thought, that it's not something that PCs can do anyway, this swapping of things ? And that it would be (as @Lanefan says) a bad precedent to allow it in cases like this as it would "create a precedent" ?
It seems common in games I've been in to use rule 0, which you mention upthread, to let players modify the classes to fit their vision (a weapon proficiency they might not have by RAW, a different spell list for their cleric, etc...). Merchant training instead of a bunch of class skills seems ok (but I might warn the player that those skills might be much less useful to the party than some others).
But then, by doing that, you are already saying that the merchant has at least one level in a PC class, with everything else that goes with it including other more combat orientated proficiencies that he does not have any reason to have.
So actually, simply by forcing this at start, you are undermining the consistency of the character as he needs to function in the world.