The speed of this(or any) program depends on the state of the SD card and it's health. On one hand, a class 2 rated card will be slower than, say, a class 4 or 6. On the other hand, a card that has been used for a while with repeated read/write cycles will be slower than a similar card that is new. Eventually a card will become read-only, this is the nature of flash-based memory.
In my opinion, if a card is that slow as to become unusable, it's time to replace it and not look back. If you believe the card still has some life in it, you can let it run overnight until the program has finished it's job. The purpose of this whole thing was to remove a stubborn virus from it. Any program you'll use will imply some write cycles on the card, hereby shortening somewhat the life span of the card itself (see above). If the card is somewhere at the middle of it's life span, it will not make any difference, but if it is dying, better to replace it, because this will push the card a little further down it's road.
Killdisk is writing zeroes on the card, rendering it in a clean state. Any other program that does that will do fine. As I have said in a previous post, you could use the formatting utility that comes with the phone (if comes with one). Formatting does NOT erase the card, though, you might end up with the same virus.