The Scion template, in a kitchen-sink setting such as the Dresdenverse, already allows for virtually free reign in designing the powers selection of a character if the player is willing to put a mild effort into planning and the creation of the 'parent' entity, so that's no issue. Moreover, Scions are not inherently beholden to any higher authority (though one may try to impose their rule upon them, as with many Changelings), so the lack of such a relationship is not itself an issue.
The only issues (aside from the Wizard's Constitution & refresh cap that you mentioned) I forsee are those of the tone of the game, which will already vary from one table to another sufficiently that I do not see any inherent problem with this template in that regard. I would advise caution in its use, of course,
On a larger scale, I, personally, do not see particular purpose in the use of Templates at all save as 'cheat sheets' for new players that have trouble when presented with too many options. For my own purposes, and those of other players I know to be sufficiently experienced, I suggest simply requiring that any and all powers (and even stunts) chosen are supported by the character's aspects, most importantly by their High Concept. With a good understanding reached between the player and the GM at the time such an aspect is created (ex. during character creation or at an appropriate milestone), the lists of 'musts' and 'options' presented by Templates become wholly obsolete.