I have had a similar problem in early game moon missions.
Try adding as many static fins as you can and be sure to keep away from the time warp button
Even some of my small craft would survive the flight but if i hit the time warp all hell breaks loose.
Here is an idea - Please backup your files before you go editing CFG's
In general all configuration files required for this are in a subdirectory of GameData. Itself is a subdirectory of the root directory.
When you find the folder GameData, open it
From here you will find two other folders. The "NASAmission" folder, and the "Squad" folder.
You may see more folders if you install mods for KSP. The "NASAmission" folder contains all the parts created with the help of NASA in the most recent update, like the four block engine, or the Launch Escape System. The "Squad" folder contains most of the stock parts, like the Command Pod Mk1, or the Mobile Processing Lab. go ahead and open the "Squad" folder.
From here, you will find the folders containing just about every object in the game. Since you are editing parts, open the "Parts" folder (obviously). There is also a "SPP" directory which contain the parts from the Spaceplane+ mod integrated in 0.25.
From there, you will find more folders, each one representing a tab in the Vehicle Assembly Building
So now you will need to look at your crash details (what fails first) and find that part's folder, inside that folder you will see partname.cfg
open it up in a text editor - notepad or whatever
and do a search for "Standard part parameters tab"
What you are looking for is the breakingForce parameter.
I am at work right now so i cant test if you will even find it in there as i only ever play with my crashTolerance but all the parameters should be in there. I do know however that if you do find it it may be set to 1.0 which seems to directly scale to 50 Kilonewtons of force.