Aziere, you are completely right.
Couple of workarounds for the meantime:
/bind MOUSE2"+button5; +zoom"
Press and hold zoom, then press and hold fire, release zoom to fire. Pretty crappy, but maybe better than an extra key.
A better option is to add re-binds to your buy weapon scripts if you use them. I didn't even think to do this until reading this thread, so thanks.
Here's my buy weapons script, it works great. The only secondary attacks you need are luci and ckit.
//shop weapons
bind 1 "sell weapons; buy psaw"
bind 2 "sell weapons; buy rifle"
bind 3 "sell weapons; buy shotgun"
bind 4 "sell weapons; buy lgun"
bind 5 "sell weapons; buy prifle"
bind 6 "sell weapons; buy mdriver; bind MOUSE2 +zoom"
bind 7 "sell weapons; buy flamer"
bind 8 "sell weapons; buy chaingun"
bind 9 "sell weapons; buy lcannon; bind MOUSE2 +button5"
bind 0 "sell weapons; buy ackit; buy ckit; bind MOUSE2 +button5"
The only problem with this is if you die after buying a mass driver and spawn with a ckit, you will have to hit your "buy ckit" key to enable the repair function.
edit: Here is yet another option, in case you don't use buy weapon binds... Right now you hold x to zoom and it sucks. Instead, why not tap x to swap the function of mouse2:
set mzoff "bind MOUSE2 +button5; bind x vstr mzon; echo mousezoom off"
set mzon "bind MOUSE2 +zoom; bind x vstr mzoff; echo mousezoom on"
// off by default so that ckit works
vstr mzoff
yea, these are hacked together workarounds, but they'll work while we wait for the fix (assuming it gets fixed

)