The Eagle is primarily a cheap harasser.
It can be fitted with 3x C2 Cannons and still have a 5.44L/yr jump range which is enough to navigate the closer systems where small fighters and harasser craft are required.
The Eagle agility makes it perfect for combating larger ships that don't have the ability to turn anywhere near as fast as the Eagle, allowing it to effectively cripple the ship's components to a point that the ship it no long combat effective.
The speed of the Eagle is something that sucks, yes, but it's not designed to be extremely fast, that's the viper's job.
The Viper is a heavy attack craft, with the capability to house powerful weapons and get from point A to point B with extreme speed if required, but at a penalty. The Viper can EASILY over shoot targets that have higher maneuverability, which causes it to boost back out and make another run.
The Eagle keeping the Viper busy seems to be the purpose of this craft. A smaller, more agile ship, keeping a bigger and more powerful ship at bay whilst other ships complete the objective. ( IE: A mouse keeping the cat busy the the rat can eat the cheese.)