The PCs are heroes. Everything is OP against generic, nameless NPCs.
Plus, you don't need to let him spam.
I run a weekly Saga Edition game via IRC, and I've seen that second problem a lot. When it comes to making skill checks when there's plenty of time, players will always say... "Ok, but can I try again?" My answer, as part of my GMing style? "Not unless something meaningful changes - that's what taking 10 and taking 20 are for."
But my own house-rule doesn't have to apply, when it comes to Force power spamming. Where you're getting the cooldown from is probably here (Core rulebook, page 95, emphasis added):
- When combat is over and you've had a minute to rest for 1 minute, [...]
This particular clause isn't fully explained, nor is it addressed in the official errata. Does this mean Force powers, even if used during down-time, only come back after a fight? Probably not. What it does convey (absent any mention in said errata), is an intent specifically against Jedi having the same powers continuously at their disposal, to be used again and again. It's your call as a GM, and reasonable players will agree that an auto-win button isn't much fun - where's the game, the tension, and the drama? I like to borrow a page or two from a more 'cinematic' system, like Fate, and say the whole encounter with the merchant (or any other social encounter) is a 'combat' itself, and they don't get their powers back until it's decided one way (full price, take it or leave it) or another (discounts I wouldn't do for anyone else, but not everything I own!).
Moving on to whether and how this power is OP, let's look at another use of it that makes it more so: the ability to cause people to flee in terror! While your players have apparentl siezed on the usage that will "make an otherwise unpalatable suggestion seem reasonable" (which is up to your discretion, and should probably include the opponent's attitude... which, given the Special as MrTumnus mentions requires a precious Force Point to activate, might be worth giving to them if they're that invested), there's another one that I consider more OP against nameless NPCs:
- You fill the target with terror, causing it to flee from you at top speed for 1 minute. [...]
You want a show-stopper? There's one right there. While this particular usage doesn't work if the target's the same level or higher, for a specialized Force user it's an amazing, almost sure way to get rid of a minion every round until there are no more. Not to mention looting a merchant's goods.
Is that balanced with what your average blaster-toting soldier thinks they could do? Probably not, especially if minions are a big feature in your battles. But let's not forget what a Noble could do in this system, particularly with feats like Silver Tongue or Presence, and being as focused into Persuasion as this Jedi seems to be in Use the Force. You look at what some of the Noble talents let you do with Persuasion, and it can seem OP pretty quick. But against the same minion-composed enemies, your Soldier probably has an Autofire weapon, with which to mow them down.
So finally getting back to your non-combat situation and short-circuiting of the campaign, I'd like to first point out the rules for giving out Dark Side Points on pages 93-94. The power says the PCs are incapable of making the target knowingly endanger himself, but the morality of the Force also has something to say, here. In particular, I would call swindling a merchant out of some of his wares something of a dubiously evil act, at least, under the Minor Transgressions heading (worthy of DSP if it becomes a pattern), and moving up the scale to a Moderate Transgression would be if it unduly hurts the merchant - "give me all your money, but I don't have an immediate need for it" sure stinks of the Dark Side's selfishness to me.
Perhaps the players are opting to take the campaign dark more quickly than you expected, but as long as you're all having fun, that should be fine.
There's also, of course, environmental effects and other Force users to worry about, but that's just waiting to write itself.
I mentioned nameless NPCs. Recall Phantom Menace, where Qui-gon is unable (despite his cavalier attitude and willingness) to mind-trick Watto? It may seem a bit thin, but when your campaign rides wholly on this, it's an option. Another would be to give the NPC a name, a backstory, and some PC class levels - like the well known D&D trope of the Bartending Former Adventurer. Who's to say the merchant is the right CR for them to take on? And who's to say he's not purpose-built to be a shrewd negotiator? ...but on that note, if they do take him down after all that, what a great story! It can be much more fun than That Guy That Mindlessly Gives Money, while the occasional Guy That [Doesn't] Want[s] to Sell Death Sticks might also be good for a laugh.
And for completeness, absolutely, MrTumnus' answer regarding Mind Trick's suggestion usage not being Mind Control. Consider in Empire, when Luke has Bib Fortuna, Jabba's majordomo and head of day-to-day operations under the sway of this power. Why not say, "You will discreetly bring the following people to me," rather than blundering into the Big Boss, who also happened to be immune to Mind Trick? Well, according to in-universe canon (near the end of the page), it was because Luke had to play on Bib's existing motivations, adjusting the different weights of his priorities.