While I don't see much issue with the entire thing (it seems more of a DM issue, since he introduced the guard in that position and could have just as easier said the guard didn't run or is surprised, or some variety), however, since it's clearly an issue with some people and the () doesn't work for some people, who prefer a dice-based response, or a "he wouldn't do that" response, I think a recap of all the issues at play would be beneficial in order to see what the real issue might be.
1. Distance vs thrown weapons
2. The Run Action (or even the 2x move action)
3. Initiative
4. Readying an action
5. Surprise
Did I miss anything?
1. This is an issue because of the 5' grid system. 10 feet away feels further in real life than on a 5' grid. It never really seems beneficial to throw a weapon in D&D when you can just step 5' and make a full attack action. The OP seems to want to recreate the feel of the scene in Apocolypto when the characters are running from the other group throwing spears. In D&D the throwers would get maybe one throw before the characters are out of range and that's only with a readied action. Either the range needs to increase for thrown weapons to compensate for the grid system (even if it's only a 10' range increase) or the grid system needs to decrease to 2 or 3 feet.
2. Their should be very few situations where the run action can be used (straight line, no difficult terrain, etc). It doesn't present itself very often, but when it does, it's usually the baddie making a run for it. I don't think splitting up movement will really get at the issue here. Maybe something like using the Run Action provokes attacks of opportunity from ranged attacks? If a character has a bow, crossbow, spear, handy, then they get an AOO on the person engaging in the run action. This doesn't mesh well with other actions and AOO from ranged weapons, but it does perhaps solve the issue. Although until you've gone in initiative you also don't get to make AOOs. But if you're breaking the AOO rules anyway, why not take it all the way
3. Initiative. It's not to difficult to gain a huge bonus to initiative (High teens are not uncommon in some of the games I've played). This makes any character who doesn't invest in initiative feel like they're always going last. Others have presented alternatives which seem to be more involved than a simple roll and turn-based system. It's not uncommon either for the character in the back to go first and have to either move through all the other characters, hold their action, or gain penalties to ranged attacks. I believe that earlier editions allowed for the us vs them initiative, but that doesn't seem to resolve the issue. You could use a cluster system to determine initiative (Initiative bonus 1-5, initiative bonus 6-10, initiative bonus, 11-15, etc., and then the clusters roll off to determine who does first within each cluster). Seems a bit too complex for my liking and I'm not sure that would help either. There's the ranged weapon attacks go first, followed by melee, followed by spells, followed by only movement system, but that just doesn't feel right. I don't know if there's a good single system for initiative, it's really up to the group to determine what feels right. I'm not sure any fix for initiative would really solve the OP issue.
4/5. Readying an action and surprise. You're not really suppose to have a "readied" action prior to the rolling of initiative, but sometimes it just makes sense. How else would you do a sweep of a building? Move/Ready, Move/Ready, Move/Ready, Fire. This would still need to be declared in some way, and it would slow down exploration (like searching each and every 5' square for traps and treasure). I don't think Readying an action is really suppose to counter the Surprise action either and if you're readied for an ambush (if you're strolling down a path) then it makes ambushing impossible. I don't think either of these would have solved the OP issue.
Anyway, those are just some of my thoughts. I hope you find a way to make it work for you. There's nothing more frustrating than someone making a run for it!