An alternative to changing the order of summation is to change a sum and an integral (no, it's not that different...). It is well-known that
$$ \zeta(s) = \frac{1}{\Gamma(s)} \int_0^{\infty} \frac{x^{s-1}}{e^x-1} \, dx, $$
which we can prove by expanding the denominator, using the binomial theorem on $e^{-x}(1-e^{-x})^{-1}$, which is perfectly fine since $|e^{-x}|<1$ for $x>0$; we then use the usual gamma integral. This immediately suggests a related formula for $\zeta(s)-1$: adding an $e^{-x}$ to the numerator just means we expand $e^{-2x}(1-e^{-x})^{-1}$, with the obvious result. Hence we can sum
$$ \sum_{k=2}^{\infty} (-1)^k(\zeta(k)-1) = \sum_{k=2}^{\infty} \frac{(-1)^k}{\Gamma(k)} \int_0^{\infty} \frac{x^{k-1}e^{-x}}{e^x-1} \, dx. $$
Interchanging the order of summation and integration, we arrive at
$$ \int_0^{\infty} \frac{e^{-2x}}{1-e^{-x}} \sum_{k=2}^{\infty} \frac{(-1)^k}{\Gamma(k)} x^{k-1} \, dx = \int_0^{\infty} \frac{e^{-2x}}{1-e^{-x}} (1-e^{-x}) \, dx \\
= \int_{0}^{\infty} e^{-2x} \, dx = \frac{1}{2}. $$
Edited to add:
This generalises nicely to sums of the form
$$ \sum_{k=2}^{\infty} \binom{k-1}{r} (\zeta(k)-1) = \zeta(r+1); $$
the alternating sums seem to lack such a simple expression, but can also be expressed in a similar way.
Edit 2:
Further work reveals
$$ \sum_{k=2}^{\infty} (-1)^k\binom{k-1}{r} (\zeta(k)-1) = \zeta(r+1)-1-2^{-r-1}. $$