This does indeed look like an exception. I am not aware of any other verbs where the imperative polite form does not match the infinitive (but I may just not have thought of it). In any case, the polite (Sie-form) imperative of sein is indeed seien.
Canoo.net claims that there are only two imperatives: singular and plural. For sein, the singular imperative would be sei and the plural one seid. They continue to say that to make a polite request, one must resort to conjunctive I of the third person plural (capitalised to be Sie). Since they state no exceptions, it seems that ‘seien Sie’ can be perfectly rationalised with this rule. Again, I am not aware of any other verb whose conjunctive I form in third person plural does not match its infinitive.
Canoo.net’s definition does suffer from the fact that an imperative statement comes with a different word order, but it seems consistend and rational.