The phrase is not literal; you don't need to imagine throwing a stone. It signifies something is very close. The cafe is a stone's throw from her office, so she walks there for lunch.
Pro Tip 2/3
Idiomatic Nature
'A stone's throw' is an idiom; understand it as an expression that conveys proximity easily. You'll find the museum is just a stone's throw from the main square.
Pro Tip 3/3
Informal Context
This phrase is conversational and best used in informal dialogue or writing, not formal documents. Luckily, my new job is a stone's throw from home, so my commute is easy!