Currently, there's no way to indicate a a team preference during auto-scrambles.
You can however pair up with a friend using the command: sm_addbuddy in console then pick your friend's name in the menu. This will tell the auto-scramble plugin to try to put you and your friend on the same team. It doesn't always work, because sometimes teams are just too unbalanced (or you and your friend are too OP). However, you can only pair up with one other player at a time.
It's not a perfect solution (and it doesn't solve your issue), but it can be useful

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I'll look for ways to let players pick a "favorite" team for auto-scrambles in the future though.