We can try to derive the recurrence for the sequence $(F_{2n})$. (This was already suggested in the comments.) Then we can get matrix form for it, similar as the well-known matrix form for Fibonacci numbers.
This is a very natural thing to do for anybody who saw derivation of similar identity for Fibonacci numbers based on determinants.
So we first notice that $F_{n+2}=F_{n+1}+F_n=2F_n+F_{n-1}=3F_n-F_{n-2}$. So we have
$$F_{2n+2}=3F_{2n}-F_{2n-2}.$$
This gives us
$$
\begin{pmatrix}
F_{2n+2} & F_{2n} \\
F_{2n} & F_{2n-2}
\end{pmatrix}=
\begin{pmatrix}
3 &-1 \\
1 & 0
\end{pmatrix}
\begin{pmatrix}
F_{2n} & F_{2n-2} \\
F_{2n-2} & F_{2n-4}
\end{pmatrix}.
$$
So by induction we get
$$
\begin{pmatrix}
F_{2n+2} & F_{2n} \\
F_{2n} & F_{2n-2}
\end{pmatrix}=
\begin{pmatrix}
3 &-1 \\
1 & 0
\end{pmatrix}^n
\begin{pmatrix}
1 & 0 \\
0 &-1 \\
\end{pmatrix}.
$$
If we take determinants on both sides, we get
$$F_{2n+2}F_{2n-2}-F_{2n}^2=-1,$$
which is equivalent to the identity in the question.