Neutralization of ions in the ion thruster

The Problem you are assuming, is actually none:

Temporarily stored electrons are finally reinjected by a neutralizer in the cloud of ions after it has passed through the electrostatic grid, so the gas becomes neutral again and can freely disperse in space without any further electrical interaction with the thruster.

Source: Ion Thruster Wiki, just in the introduction

It is always important to keep the charge of a spacecraft close to zero and to never get too large. This is true no matter if you are using ion propulsion or not.

A charged spacecraft can suffer from several failure modes. So when a spacecraft emits positive ions it also must use an electron gun to emit electrons to keep the spacecraft close to neutral.

Rather than reproduce all the reasons and problems here, I'll direct you to the excellent discussions in the following posts:

• Strategies for combating ESD and ground plane potential shifts on spacecraft charging?
• How do spacecraft measure their own charge?
• How is charge dissipated in ion-propulsed spacecraft?
• Is a spacecraft able to measure it's current electric charge in some way?