Scout seems pretty worthles with the stock weapons
Scout's primary is by far the best. The rest are either subpar or a bit more situational. The pistol though can be swapped for a better utility like Mad Milk, and pretty much all of the bat's alternatives are better.
as Medic, I can barely defend myself.
This usually has more to do with your playing style rather than your weapons, as you pretty much have to rely on your buddies to be your meat shields. The Overdose is an upgrade over the stock when you need to escape from a sticky situation though, and the Solemn Vow helps you check if there are disguised Spies around.
As for the trading thing, pretty much all the crates are useless (save for the salvaged ones, which I would recommend to spend some bucks to unlock as you would always turn up a profit), so you can either delete it or let it gather dust in your backpack. Also each regular weapon is worth around a scrap or 2 weapons, although some users specifically gear their trades to beginners and can do 1:1 weapon trades.