Have you tried alt-double-clicking? I've noticed that a great many units will typically halt to gather themselves up for the charge when you issue a single-click attack command. When you issue a double-click attack command, though, they simply continue running and move weapons to charge position, without the long stop in the middle to regroup. The AI even seems to issue explicit run commands to troops at some distance farther away than charge distance, seemingly to avoid this exact thing. I would speculate, then, that if you alt-double-click with your archers (or start them running when they get somewhat close), they will switch weapons while running and not incur the long pause to switch weapons that you have described. More than likely they'll just draw secondary weapon and immediately brandish it for the charge when at the correct distance, continuing to run the whole time.

So while this method applies generally to melee foot troops, I suspect it will also include archers sent into melee combat.