No, efficient alternate picking, like any picking, should be done effortlessly. You're not going to get where you want to go if you're fighting yourself or the guitar. Ever see a video of Shawn Lane play? Like breating or drinking. It could be an ergonomics issue. Check your playing position (are you standing?), etc.....

Think of it like cracking a bull whip. It takes very little effort at the user end to generate amazing velocity at the other end of the whip.