The pure scientist and the pure soldier is an NPC. He is not the protagonist of the story told in the game. At best, he's a side-kick.
(That's in fact how it works in many movies - there is a single protagonist that can do a lot of stuff, but sometimes he has side-kicks that can help him out in certain areas. Of course, in a RPG, would you want to play the side-kick if your friend plays the protagonist?
You are assuming a game with either a decent amount of combat or a combat focused game. Modern was not for characters to start of as experienced Action Heroes or the assumption that the default campaign would necessarily see a decent amount of combat
THe game was designed assuming the game would automatically run any type of Modern setting game from Scooby Doo to combat focused games (and, if you want, I will actually link you to the quote at the WOTC site where Scooby Doo was stated).
Furthermore, the game is designed to start off as normal people, who grow into the hero role via multiclassing and advanced classes. If you want to do A-Team, Die Hard, Indiana Jones, or characters with an experienced background in their occupation you start off at levels higher than one (a design intention, again, which should not have had to have been explained in Modern Player's Companion).
If you want a campaign, where people have some combat role, make sure you tell your players to take a class that gives them a good BAB and/or start the game at a higher level so that they can multiclass.
If you want characters to not be focused on non-combat skills, tell that to your players. Tell them that they need to spend spend points on non-combat skills. Occupations are there to provide characters some additional class skills. So, don't let you players, get away without having some non-combat skills. If necessary starting at a higher level so that characters can multiclass is not a bad idea depending on the type of game you are running.
And, with regards to the the dedicated scientist or soldier getting caught out of their element, maybe, that is a good time to use action points for a bonus to help them succeed and an incentive to multiclass. If combat is going to be important to the campaign, the non-combat character should be multiclassing. Thnk Cordelia training in combat with Angel, Phoebe training in martial arts with Cole, Buffy (in the movie) training with her Watcher, and the new slayers training with Buffy (in the series).
Another possibility is to use cut scenes when applicable. When appropriate, provide characters things to with their specialty at different locations and cut back an forth without spending too much time with any given player at a given moment.