A negative coefficient does not necessarily entail a negative $\sigma^{2}$. Usually we do not impose positivity constraints during estimation, then we check if $\sigma^{2}$ takes some negative values or if coefficients respect some known positivity constraints (when these constraints are known).
Regarding the standard Garch model, you can force all the coefficients to be positive during maximisation of the likelihood but it is not a necessary condition (just a sufficient condition), the original formulation of Bollerslev (86) imposes this sufficient constraint. If you employ this constraint, you should not "remove" negative coefficients as they should never appear as a plausible result during estimation.
For each Garch-type of model, sufficient conditions (i.e parameter restrictions) are different, as an example see Tsai, H., & Chan, K. S. (2008) for Garch model. Egarch, GJR... have different constraints.
Tsai, H., & Chan, K. S. (2008). A note on inequality constraints in the garch model. Econometric Theory, 24(3), 823–828. http://doi.org/10.1017/S0266466608080432
Bollerslev, T. (1986). Generalized Autoregressive Conditional Heteroskedasticity. Journal of Econometrics, 31, 307–327.