In the context of its publication, The Faerie Queene was written in an anachronistic style with the use of older spellings to convey a sense of an imagined Medieval past. In the case of 'faerie', Edmund Spenser went back to French to create a more authentic (in his mind) and courtly word than the one available to him.

By the time of A Midsommer Night's Dreame (see this 1623 folio), the French 'faerie' had already given way to the Middle English 'fairie' - by way of 'fayry' and 'fayrie' - with its final destination being 'fairy'. The most common spelling around the time Spenser was published (1570) is the aforementioned 'fayrie', which is used in Edmond Bicknoll's Sword Agaynst Swearyng (1579) and James VII and I's Daemonologie (1597). The English translation of Jean D'Arras's Mélusine uses 'fayry' circa-1500 so Spenser is reaching back at least a century to grasp at an older tradition.

Bit of a tangent, but the answer is that the manner in which The Faerie Queene is written is integral to its interpretation, as the authorial intent is seen through these anachronistic language choices.