It can be bypassed with no ill effects. I believe that the carb icing circuit is only on Australian models, which makes me think that the Japanese have some confusion WRT your proximity to the Antarctic.
I, and many other Merkuns and Canadanians, have ridden KLRs in subfreezing weather (wet and dry) and have had no problem with carb icing.
BTW, that pump cover makes for a very good start of a radiator bypass system.
It truly is a mystery to most of us why the Australian & New Zealand KLRs received the carb de-icing plumbing.
Northern Europe, Canada & Alaska would make more sense.
Yes the portion which goes to and from the carb can be readily eliminated.
But as Tom sort of suggested, instead of just capping, one can connect the thermostat outlet nipple to the water pump inlet nipple, while avoiding the exhaust header.
This will make a radiator by-pass re-circulating system to allow quicker engine warm-up. A larger hose would be Great.
Are you familiar with the Thermo-Bob 2?
Thermo-Bob 2 for KLR650
You could possibly purchase a warmer 90C thermostat over in Oz and have All of the exact same advantages. Quicker warm-up, improved fuel economy, consistent performance, cleaner engine oil.