All personal auto policies have an (exclusion) that won't pay "in the course of business". If I had to guess, driving a truck, you are a pizza driver, since with Uber or Lyft, I "think" they make sure that you have a separate/business policy to drive for them and they don't/allow trucks?
Rear end, clear fault, no defense. And (NO) you owe for the FULL amount, not just a deductible. If her insurance pays, they go after (what) insurance pays Plus the policyholders deductible. Is the $6,000 estimate from (her) insurance company, or is it from her only? If, from the insurance, then it is the right amount, but if she got it, then it is (possible) it is too high. If a body shop knows that insurance is not paying, then they could charge more for labor, or instead of used parts, then charge for new parts that cost more.
What expenses is she submitting with the estimate? The only other expense she would be entitled to is for a rental car while her car is in the shop for repairs. If she is claiming lost wages to get estimate or time off work, then NO, she is not entitled for that, nor gas etc. The only time you can claim lost wages is (IF) she was injured and unable to work.
Depending where you live, in (most) states, the MAX you can claim in small claims court (no lawyer needed) is $5,000. So even if the amount is $6,000 and if the max is $5,000, then she cant get more in small claims court. "Most" states, if she gets a garnishment, then I "believe" the max is 25%.
Now (if) her insurance pays, would be better, since most insurance companies will set up a payment plan to pay back the amount that you owe, say in 12 monthly payments.
These are the facts, good luck
retired auto adjuster