The interstellar and intergalactic medium contain huge amounts of free ions (both free protons and electrons).
However, when these particles are not stabilized in an atom because they are excited, as they have the same charge, they should repel each other by electromagnetic forces, so how can they be held together and not fly away to infinity?
And in the case that proton decay is a real thing, in the far future, how will this gas held together once protons "disappear" from this medium?
If electrons were to attempt to separate, protons, being oppositely charged, would be naturally drawn to follow them due to the fundamental electromagnetic attraction. However, proton decay, while theoretically possible, occurs over such an unfathomably long timescale that all stars would have extinguished long before it could have any significant effect on matter. In such a scenario, the absence of stars and energy sources would mean that the conditions required for plasma, which depends on the ionization of atoms, would no longer exist.
If you have a cloud of completely ionised, net-neutral gas and then you try to remove some of the charged constituents - say the electrons have a higher velocity dispersion - then all that will happen is that you would make the centre more positively charged and this would provide a restoring force that would prevent the electrons leaving.
In practice you will get some charge separation in this manner until an equilibrium is achieved with the centre of the cloud having a net positive charge whilst the electrons would have a broader distribution.
As an example, the greater mobility of electrons in the solar wind leaves the Sun with a small ($\sim 100$C) positive charge. What is the electric charge of the Sun and its corona?
As for proton decay, I'm no expert on the decay mechanisms, but those proposed would generally conserve electric charge (e.g., decay to a positron and neutral pion) so really doesn't have much bearing on the problem.
