smobo's mentioned option is great in my opinion.
personally i use different configs for different loadouts, which has always worked great for me.
example: bind keys 7 through 0 to equipping loadout A-D + executing a script that supports that loadout.
in my case, when i select soldier, my 9 key becomes equipping loadout C (gunboats, RL, equalizer) and it executes soldierC.cfg.
in your case, you could do the same, and then just add a small script to soldierC.cfg (or whatever) that skips selecting slot2 with the mwheel, so your mwheel will then scroll only through slot1 and slot3.
for example, this is in my soldier.cfg:
bind 7 "exec soldier
bind 8 "load_itempreset 1;exec soldierB
bind 9 "load_itempreset 2;exec soldierC
bind 0 "load_itempreset 3;exec soldierD
(load_itempreset 0 is in soldier.cfg)
so if i select soldier, and then press 9 when in spawn, i will respawn with loadout C + execute soldierC.cfg. easy as that!