Servers are paid based on how much the customer tips, not based on the restaurant's profit margin. The fact that tips are done as a percent of the bill means that they're incentivized to point you at the more expensive side of the menu, but it's much more important to pick something that'll impress the patron than to maximize the size of the bill. The restaurant's margin doesn't directly factor into this at all.
If you think the specials at a restaurant are just designed to clean out the back of the walk-in, you shouldn't be eating anything there. By all means, though, order off the menu. Letting the server pick is a good play if you're optimistic about the restaurant.
