First of all, you need to be careful what you mean by a NOT gate. If you have only one qubit, you could use the gate (typically called X) $$\begin{pmatrix}0 & 1\\1& 0\end{pmatrix},$$ which flips the two basis states of the qubit. Since your system here consists of only one electron, this won't affect the 'spatial wave function' very much.
If you're talking about two or more qubits, you need to keep in mind that quantum operations are always done whilst (physically) identifying each of the qubits. If, for example, you'd have the following operation:
$$|00\rangle \mapsto \frac{1}{\sqrt{2}}\left[|01\rangle - |11\rangle\right],$$ that means that the 'left' bit is mapped to 0 or 1, whilst the 'right' one is mapped to 1. You're therefore never really 'swapping particles'. In fact, if you were to do quantum computing on an entangled two-fermion system, (say: a deuterium atom), how would you probe the system, i.e., how would you experimentally distinguish between $|01\rangle$ and $|10\rangle$?
What you could do, is swap the basis states of the two qubits, using a gate like
$$\begin{pmatrix}1 & 0 & 0 & 0\\0 & 0 & 1 & 0 \\ 0 & 1 & 0 & 0 \\0 & 0 & 0 & 1\end{pmatrix},$$ where the basis states are labeled $|00\rangle,\quad |10\rangle,\quad|01\rangle,\quad|11\rangle.$ [The matrix above is indeed unitary.] In fact, this quantum operation would leave the spin-symmetric states $|00\rangle, \quad |11\rangle$ alone.