I don't think you can change the color of the custom crosshair, but you can definitely bring up the ingame crosshairs and change the crosshair color with something like this:
bind 1 slot1;cl_crosshair_green 255;cl_crosshair_red 0; cl_crosshair_blue 0;
bind 2 slot2;cl_crosshair_green 255;cl_crosshair_red 255; cl_crosshair_blue 0;
bind 3 slot3;cl_crosshair_green 255;cl_crosshair_red 255; cl_crosshair_blue 255;
bind q slot1;cl_crosshair_green 255;cl_crosshair_red 0; cl_crosshair_blue 0;
something like that

you could make the hud crosshair transparent and have a tf crosshair show through the hud crosshair so you dont lose track

this^
just set fg color to 255 255 255 0

So hitsound and dmg text is not enough?

what if he/she plays without sound and hits someone around a corner

I play soldier so I don't always see damage text (spam from around corners etc). Mumble comms during serious play and music during casual pubbing blocks out my hitsound sometimes. It's just my preference D:

Mh makes sense

Replace cl_crosshair_file with an alias such as:
alias green "cl_crosshair_green 255;cl_crosshair_red 0;cl_crosshair_blue 0;"
etc.

I stopped doing this because I picked colors that were extremely hard to see if you had your crosshair on someone and instead switched to crosshair style.

Also, this is for all weapon previous weapons (aka if you press q, it'll go to melee, not like what you would want).

alias prim "slot1;cl_crosshair_file crosshair7;bind 2 1-2;bind 3 1-3;bind 1 prim"
alias sec"slot2;cl_crosshair_file crosshair2;bind 1 2-1;bind 3 2-3;bind 2 sec"
alias melee"slot3;cl_crosshair_file crosshair3;bind 1 3-1;bind 2 3-2;bind 3 melee"

alias 1-2 "bind q 2-1;sec;"
alias 1-3 "bind q 3-1;melee;"

alias 2-1 "bind q 1-2;prim;"
alias 2-3 "bind q 3-2;melee;"

alias 3-1 "bind q 1-3;prim;"
alias 3-2 "bind q 2-3;sec;"

bind 1 prim
bind 2 sec
bind 3 melee

eww binds in aliases

I don't get what's the problem. The purpose of the script is to mimic previous weapon. Also it's not exactly he wants since he wants q to only switch between 1 and 2.

alias green "cl_crosshair_red 0;cl_crosshair_green 255;cl_crosshair_blue 0"
alias red "cl_crosshair_red 255;cl_crosshair_green 0;cl_crosshair_blue 0"
alias pink "cl_crosshair_red 247;cl_crosshair_green 0;cl_crosshair_blue 119"

alias scatter "slot1;alias wepcycle pistol; pink" 
alias pistol "slot2;alias wepcycle scatter; green" 
alias wepcycle pistol

bind 1 "slot1; alias wepcycle pistol; pink"
bind 2 "slot2; alias wepcycle scatter; green"
bind 3 "slot3; alias wepcycle scatter; red"
cleargui

bind q wepcycle

took this from my config and changed it a bit, should work. added three colors (green red pink). this will work with quickswitch (q). Q will never switch to melee.

Thanks for the responses everyone. turtsmcgurts solution was the closest to what I was looking for. I picked crosshair1 and enlarged it so that the lines are spaced out enough to be visibly separated from my main crosshair and changed the colors to my preference (green for primary, yellow for secondary, cyan for melee). Q functions normally and I still have my custom crosshair. Thanks again!