We make use of a subtraction procedure, introduced to overcome double--counting problems in beyond--mean--field theories, in the second random--phase--approximation (SRPA) for the first time. This procedure guarantees the stability of SRPA (so that all excitation energies are real). We show that the method fits perfectly into nuclear density--functional theory. We illustrate applications to the monopole and quadrupole response and to low--lying $0^+$ and $2^+$ states in the nucleus $^{16}$O. We show that the subtraction procedure leads to: (i) results that are weakly cutoff dependent; (ii) a considerable reduction of the SRPA downwards shift with respect to the random--phase approximation (RPA) spectra (systematically found in all previous applications). This implementation of the SRPA model will allow a reliable analysis of the effects of 2 particle--2 hole configurations ($2p2h$) on the excitation spectra of medium--mass and heavy nuclei.