The flight evolution does not work like the Fly spell
Simply because it's magical flight, it does not mean that it works like the magical Fly spell, but that its a Supernatural ability. The evolution description is the following:
Flight (Ex or Su): The eidolon grows large wings, like those of a bat, bird, insect, or dragon, gaining the ability to fly. The eidolon gains a fly speed equal to its base speed. The eidolon’s maneuverability depends on its size. Medium or smaller eidolons have good maneuverability. Large eidolons have average maneuverability, while Huge eidolons have poor maneuverability. For 2 additional evolution points, the eidolon flies by means of magic. It loses its wings, but its maneuverability increases to perfect. If the eidolon flies by magic, this is a supernatural ability. The eidolon can increase its fly speed by spending additional evolution points, gaining a 20-foot increase to its fly speed for each additional point spent. Requirements: Summoner level 5th.
Now, regardless of the ability type or the source of this flight speed, this has nothing to do with the Fly spell, which has specific rulings on how the spell works. If you check the movement rules, there is nothing that prevents a flying creature from taking the Hustle or Run movement types.
That restriction is specific to the Fly spell and does not affect any other source of flight that is not based on that spell.
However, flying creatures were allowed to run back in 3.5, because the monster manual specifically said so, but that rule reference is missing in Pathfinder, which confused some people. There is an open FAQ request thread at Paizo's messageboards asking for official clarification on that topic.
Personally, I don't try to backtrack Pathfinder rules to 3.5 rules, unless the reason behind a rule is certainly mysterious, and as I read the rules now, a flying or swimming speed is no different from a land speed. While back in 3.5 you had to memorize or pick up the book to figure out if each creature could run or not.