The military’s stake in the Egyptian economy certainly has to be dismantled before the army can have anything like a normal role in the country, but of course, the question is who will take over the army’s holdings? Will it be the State, or will it be foreign investors or the Egyptian private sector?
There are two problems here.
The military seized the government in response to the threat of Neoliberal reforms which they correctly feared would dispossess them of their assets and divvy them up among foreign corporate plunderers.
Taking control of the process of neoliberal reforms allows the army to keep their own interests intact. You can potentially remove this motivation by destroying the military’s economic assets (its companies, facilities, factories, etc), thereby eliminating their stake in the economy, and therefore, their motive for managing the neoliberal process. Basically, remove the military from a role in the economy by annihilating their interests. There are many ways to do this.
But your next problem is the neoliberal process itself, which will, of course, continue. And there is no reason to believe that the army will not be enlisted to enforce this process on behalf of multinational corporations and investors.
So, no, the main issue is not the army itself, but the interests which it is being utilized to serve and secure. Even if you were somehow able to decimate the army, the interests will still be there, and will still be served and secured, perhaps by private military contractors, perhaps by international troops, perhaps by ISIS-style militias and death squads as in the original Latin America model of neoliberal domination.
There is no way to resolve the crisis of sovereignty except by confronting the corporate imperial system.