Please do check the column specifications and it's compatibility with the said compound. You can easily get this info on respective column supplier's website .

I would not inject it, the stationary phase you will used can be oxidized. Try to destroy perchlorate with a reducing agent.

Let's have a look  at the properties of TBAperchlorate first:

Tetrabutylammonium perchlorate Chemical Properties

Melting point 

211-215 °C

solubility 

acetonitrile: 0.1 g/mL, clear, colorless

Water Solubility 

Soluble in acetonitrile and ethanol. Very slightly soluble in water.

Sensitive 

Hygroscopic

Stability:

Stable. Strong oxidizer - contact with combustible material may cause fire. Incompatible with strong reducing agents, combustible materials. Do not heat.

As you can derive from the high melting point the compound is not volatile. and will not reach the ms and most likely even not the column. With each injection there will be a build up of non reacted TBAperchlorate in the injector liner however.

In the properties you find hygroscopic, strong oxidizer and 'do not heat'

-first the do not heat

This product may thermally decompose in a violent way depending on the amount present. So if you inject at a sufficient high temperature this will occur on each injection creating a pressure wave witch will be handled by the split. there is no build up and reaction products  reaching the column are the only concern, you could use a guard column. If the injections are below the decomposition threshold, the collected material from several injections may decompose first time a higher temperature is chosen. Depending on the collected amount  there could be damadge

- strong oxidizer

if there is unattended build up in the injector and you would use an oxidizable solvent like methanol this solvent will be oxidized immediately in a violent way

-hygroscopic

If there is build up and the injector is left below say 100°C water may be accumulated in the injector . On next use this water will be transferred to the column . Most columns don't like water

All by all it is possible but you have to be aware of the risks involved, all problems are situated at the injection liner. Injecting non volatiles leaves you with a dirty liner. 

A work around towards the oxidative power would be to add an exes of volatile oxidizable product like methanol after your sample prep but before injecting to make sure no tbaperchlorate is injected (verify the reaction products of this neutralization)

Some of the GC columns are not compatible with water. Please check column manufacturers instruction. Repeated injection of aqueous sample will ruin the column.