If you think the prima facie case against Bibi and Gallant is convincing, the Israeli AG is quite plausibly doing so little that subsidiarity is no longer engaged. If you think it is unconvincing, as you say, the problem is not some inappropriately symmetric ignoring of subsidiarity but that the charges themselves are unconvincing.
A final point is that the Rome Statute does not prohibit merely ‘orders of directly targeting civilians’, and so other potential crimes must be considered. These include ‘cruel treatment as a war crime contrary to article 8(2)(c)(i); [e]xtermination and/or murder contrary to articles 7(1)(b) and 7(1)(a), including in the context of deaths caused by starvation, as a crime against humanity; [and o]ther inhumane acts as crimes against humanity contrary to article 7(1)(k)’. Of course, you may think that Khan has jumped the gun on each of these in that each of these charges is also implausible, but that is a stronger position than doubting that there were orders to directly target civilians.
(edit: I should add that Khan [I imagine] and I would say that while subsidiarity may not preclude proceedings against Israeli officials because of Israeli inaction, Hamasnikim are not subject to anything that remotely resembles a judicial system worth the name, so there is nothing comparable to even fail to act.)