Islam and Sikhism are not comparable. Islam's fundamental tenets ensures that any Muslim population will be a perpetual threat to normal people (non muslims). Sikhism's tenets are fine. So unlike radical Muslims, who simply follow their religion, khalistanis are idiots who don't know their own gurus or religion.
This means khalistanism is a fixable problem once you remove the propaganda targeting them, unlike jihadism, which will be there as long as the religion of peace is there.
And yes, it means that a small percentage of khalistanis cannot be used to paint Sikhs in general with the same brush. Clichéd line, I know. But it's true for Sikhs. It's not true for Muslims.
EDIT: I meant to address this to
@Vinash
quoted your post by mistake.