Disabling nether portal functionality

You can use execute's detect syntax to increment a score while a player is inside the portal. Set up the objective:

/scoreboard objectives add portalTimer dummy

Create a Repeat/Chain command block line (Fill clock in 1.8), and put the following commands

/scoreboard objectives remove @a[score_portalTimer_min=1] portalTimer 1
/execute @a ~ ~ ~ detect ~ ~ ~ minecraft:portal -1 /scoreboard objectives add @a[c=1] portalTimer 2
/tp @a[x=<x1>,y=<y1>,z=<z1>,r=10,score_portalTimer_min=60] <x2> <y2> <z2>
/tp @a[x=<x2>,y=<y2>,z=<z2>,r=10,score_portalTimer_min=60] <x1> <y1> <z1>
/scoreboard players set @a[score_portalTimer_min=60] portalTimer 0

The first two commands will increase portalTimer by one for every tick for all players within the portal, and decrease it by one for players outside a portal (to a minimum of 0).

The third and fourth command teleport players that have been in the portal for 3 seconds. Replace <x1> <y1> <z1> and <x2> <y2> <z2> with coordinates just outside (!) of the first and second portals.

The last command resets the timer after teleporting. This shouldn't be strictly necessary, but it's better to have at any rate.

Check out this video.
It is basically a timer system where milliseconds before the player is teleported to the nether, they are teleported to another overworld portal instead. You can also do this with dispensers holding either mobs or items, that would instad fall on a pressure plate.