The Seeker Missile is resolved at BS5, as per the rules and the latest Tau FAQ*
Q: If a Tau Vehicle is forced to make Snap Shots fires a seeker missile using a markerlight counter, what Ballistic Skill does this shot use?
A: Ballistic Skill 5. If the target is a Zooming Flyer, resolve the shot as a Snap Shot as normal, unless it is fired by a vehicle with a velocity tracker, in which case the missile can use the Skyfire rule if you wish.
The Markerlight entry details the exact mechanics required for a Seeker missile to be used (Codex: Tau Empire, p122). It describes how it is used, and how it differs from the normal shooting rules, and the key part (in relation to this question) is "is resolved at Ballistic Skill 5". This is important because regardless of the normal BS of the model firing the Seeker, it is resolved at BS5. This means that no matter what the normal requirements are for a to-hit roll (and any modifications to the targets base BS) it is resolved at BS5. (So if it helps, think of it as not the model firing the missile, but the missile guiding itself).
It's a case of a specific rule trumps the general rule. The general rule is that jinking models can only fire Snap Shots (as per the BRB). The Specific Rule is that Seeker Missiles fired due to Markerlights are resolved at BS5. It's a similar function to the Counterfire Defence System (Overwatch at BS2 instead of BS1) or the Dark Angels detachment/formation bonus to Overwatch.
**Please note that this links to the BoLS article. GW are in the processing of "releasing" a lot of "draft" FAQ's that, while not appearing in the normal repository, are found on the official FB page, where all these images are from.