Well, firstly, I would eliminate the JS right away because you don't really need it and it'll cause you to lose ad revenue when people without it turned on visit your site. If the link is set to rel no-follow, would should be enough to stop the bots well enough though.
Aside from that, it really depends on your relationship with the 3rd part site. If you have a contract then that contract will tell you weather it is better to get as many hits as possible or weather conversions are needed. Beyond that, you've basically answered your own question as far as WHY one option is better than the other.
A lot of thought goes into weather or not it is better for a site to have a tons of random links to a site, or, if it is more important to have 'quality' links. In the end I think that as long as those links are NOT on the same server it is probably technically better to spam everywhere you possibly can to raise your rank. Just be careful, it isn't going to be worth it if you piss your users off with a bunch of spam (unless the 3rd party Co is paying VERY well). I guess it pays to ask the question, 'Where is my bread buttered?' and 'whom would I like to butter my bread?'. If your site has many loyal followers it means that you risk losing them with a move like this. If not, then no one wants to pay for your link in the first place.
