Should I unify two similar kernels with an 'if' statement, risking performance loss?

You have a third alternative, which is to use C++ templating and make the variable which is used in the if/switch statement a template parameter. Instantiate each version of the kernel you need, and then you have multiple kernels doing different things with no branch divergence or conditional evaluation to worry about, because the compiler will optimize away the dead code and the branching with it.

Perhaps something like this:

template<int action>
__global__ void kernel()
{
    switch(action) {
       case 1:
       // First code
       break;

       case 2:
       // Second code
       break;
    }
}

template void kernel<1>();
template void kernel<2>();

It will slightly decrease your performance, especially if it's in an inner loop, since you're wasting an instruction issue slot every so often, but it's not nearly as much as if a warp were divergent.

If it's a big deal, it may be worth moving the condition outside the loop, however. If the warp is truly divergent, though, think about how to remove the branching: e.g., instead of

if (i>0) {
    x = 3;
} else {
    x = y;
}

try

x = ((i>0)*3) | ((i<3)*y);