no, don't do that. That's no fun.
Here's what you do to fix the problem. It's a bug with the way FS Open 3.6.9 handles the "Red Alert" tag on missions. Hopefully it'll be fixed in 3.6.10. Anyway, get a program called "VPView." Run Turey's installer, and only download the tools and utilities instead of the whole game. VPView is included in that. Next, (and you'll have to do this on A LOT of missions) use VPView to open the homesick.vp file and extract the missions that give you this trouble. Place the extracted mission file in Games/freespace 2/data/missions. Next, open them with either notepad (changing Red Alert from 1 to 0) or FRED2 Open (and go to editors>mission specs and unchecking the Red Alert box). That'll solve that problem. Remember to repick your ship and loadout for these missions, as it will no longer carry over.
Also, some Red Alert missions will load fine, but sometimes ships that are important will have all subsystems destroyed at the very beginning. Watch out for this, too. And if you ever get a mission where, after you've removed the Red Alert tag, it crashes during the briefing (it will most likely happen), load the mission in FRED again and go to Editors>Briefing and just delete stage 1 of the briefing, and it should work fine.