There's still the question of why Mobiquity pulled their client list from the website. That's either an eyebrow-raising coincidence, or they're not cool with casual visitors knowing there's a business relationship.
The author of the blog post states that he had to go to Google cache to find the page in the first place, so there's no telling how long ago it was removed from Mobiquity's site. A past affiliation does not imply an ongoing one.
It would make no sense for them to remove the entire page when they could just remove the Starbucks logo, so it could ell just be a restructuring of the site.
Considering both Starbucks and Mobiquity are actively promoting Jonathan's Card, I'm inclined to believe the relationship is ongoing. (Frankly, this is the kind of thing that companies like Starbucks usually aren't cool with if they don't originate internally) But you're right, it is ambiguous.
I don't think it's unreasonable that they'd have responded by deleting the page, though. It's the fastest and easiest option, (perhaps the website admin isn't available) and excising the Starbucks logo alone would look awfully suspicious. Seems like exactly the thing someone would do on the spur of the moment during an "oh shit" moment when they realized a viral marketing campaign might be compromised.
It isn't at all something a company would be against if they didn't originate it - it's good PR with no downsides. They wouldn't care if every Starbucks coffee sold from now for the next ten years was paid for with one duplicated card, as long as somebody was paying for it all through that card.
Most companies like enthusiastic customers, so long as they aren't too enthusiastic. Marketers like customers who respond to campaigns, but they get very nervous when customers take control of the brand on their own initiative. It sometimes ends up taking the brand in a direction the owner would prefer it didn't go. (eg. Cristal, Burberry)
In this case, you've got multiple people sharing what should be an individual account and the potential for damaging mainstream media stories if people feel like they're doing a good turn for strangers, only to have scammers empty the card. Not to mention that if Jonathan's Card is genuinely unconnected to Starbucks, his use of their trademarks would make the lawyers uncomfortable.
This may not be a full-fledged viral marketing campaign, but I'm skeptical that Starbucks would be so enthusiastic about it if the guy responsible didn't have a preexisting relationship with their marketing department.
In my experience in marketing (tech and gaming related, so admitedly not exactly the same area), most companies I've worked with go to sleep at night dreaming of something like this happened.
Somebody who loves your company showing initiative and doing something interesting that creates headlines for your brand? And you're not paying the tens/hundreds of thousands that it would have cost to get some firm to think of this idea? Hell yes we'll take that.
It could be a move to have Starbucks disassociate themselves with Mobiquity. Perhaps Mobiquity didn't have permission to use their logo or name them as a client. If Jonathan's card brought it to Starbucks' attention, that could precipitate this kind of rapid rewriting of the web.
Assuming you've jumped from correlation to causation, trying to guess at the reasoning behind it is just that, a guess.
It would make no sense for them to remove the entire page when they could just remove the Starbucks logo, so it could ell just be a restructuring of the site.