I've also had this problem frequently, and there are several possible solutions.
The easiest one has already been pointed out, uncheck the Warp To box for the waypoint you want to bypass. However, after the combat you will still have the guidance towards Waypoint 4, in your example. And the sim will calculate flight time and fuel consumption from the position where you warp via WP 4 to WP 5.
Another way to handle this would be to plot WP 4 just a mile or two past WP 3. Create an event disabling warp at WP 3, and show a message instructing the player to maintain the present heading and only to proceed to the next waypoint when ready to return to base. Next spawn the combat that you want to happen, delay three or four minutes and enable warp.
When the enemy planes appear the waypoint guidance is hidden, and when it is displayed again after the combat you have waypoint guidance to WP 5, warp enabled to this waypoint, and correct flight time and fuel burn.
My preferred method however, is to use an alternate route. Plot your route, and then plot an alternate waypoint next to WP 5, and more beside all other remaining waypoints you may have on the way to base. Make sure you uncheck the Warp To box at WP 5 and all further waypoints of the original route. I'd also hide them to avoid confusion on the briefing map. You cannot warp to the first waypoint of an alternate route, so you must place a second waypoint next to the first one, and tick the Warp To box.
Now create a similar event as described above at WP 3. Disable warp, spawn the desired action, delay a few minutes and then change the route for the player flight and enable warp again.
So when you reach WP 3 you initially have guidance towards WP 4, but cannot warp.
At some point the enemy planes appear and waypoint guidance is hidden. During the fight the waypoints will change to the alternate route, but since they are hidden you won't notice. After the action you have guidance to the first waypoint of the alternate route, which is located next to the original WP 5 and warp is available to this point.
This method involves a little more work, but in my opinion is quite elegant and well worth the extra effort.