Well, the situation is a combination of two bugs.
First of all there's the bug where your soldier keeps on performing the left, middle or right mouse-click action. Because you mostly use the left mouse button (for firing), your Soldier will mostly keep firing though you're not clicking. Another type of this bug is that you immediately fly up with jets though you're not clicking. So in realistic mode, it is possible that your soldier is still firing, which will kill the teammates that spawned on top of you. You can stop your Soldier by pressing the button again. So if he's firing, click your left mouse button, and if he's flying click your right mouse button.
The second bug is the bug where your Soldier fires when you click - even though the weapons menu is opened. In normal mode, this bug is hardly affecting the game, though you can sometimes hear a barret firing at the rate of knocking fists. In realistic mode however, you sometimes knock or fire when you select your weapon, which will kill a teammate.
I sure support this bug report, and I hope it will be fixed in 1.4.1. I'm only afraid that there are so many bugs to fix that still alot of them will not be fixed because they've been forgotten.
Grtz, DePhille