When googling this problem myself, I found the highly-cited article
Terza, J.V., Basu, A. and Rathouz, P.J., 2008. Two-stage residual inclusion estimation: addressing endogeneity in health econometric modeling. Journal of health economics, 27(3), pp.531-543.
which proposes to use a method called 2-stage residual inclusion (2SRI) for the general linear model case. The method is very simple: Fit the first-stage model to get the residual and include both the residuals and the endogenous variable in the second-stage model.
Or more formally, let $_2$ be the endogenous variable, $_1$ till $_8$ the other exogenous control variables and $_1$ and $_2$ two instruments for $_2$. In the first stage, $_2$ is explained using linear regression
$_2=_0+_1 _1+_2 _2+…+_8 _8+_9 _1+_10 _2+_2$,
with $$ as coefficients and $_2$ as error term. The equation splits $_2$ in an exogenous component $_0+_1 _1+_2 _2+…+_8 _8+_9 _1+_10 _2$ and omitted-variable component $_2$. The 2SRI method includes both the endogenous variable $_2$ and the residual $_2$ as estimator for the omitted variable in the model; i.e. $_1=logit(_0+_1 _1+_2 _2+…+_8 _8+_9 _2+_10 _2 )+_1$
with $_1$ being the dichotomous variable. The implementation with a statics software is straight forward. (However, getting the standard errors for the estimators is not.)
It has been shown by
Burgess, S., & Thompson, S. G. (2012). Improving bias and coverage in instrumental variable analysis with weak instruments for continuous and binary outcomes. Statistics in medicine, 31(15), 1582-1600.
through a simulation that the 2SRI is better than 2SLS to provide another reference.