OK, if you can consistently reproduce the problem and reduce it to an MWE (minimum working example) then you may want to create an issue for it at Github. Then you can interact directly with the Juno developers and follow progress as it gets discussed and fixed. Or perhaps they’ll explain why this actually isn’t a problem with Atom/Juno. You never know. 
Concerning prompting, note that you can also define a short Julia function in one line like this:
sayhi(name) = println("Hi $name, how are you?")
And call it as before:
julia> sayhi("Kent")
Hi Kent, how are you?
With the convenience features of the REPL (like up arrow to bring up and edit previously typed lines) it becomes easy to re-run a function a number of times with varying input. And to benefit from Julia’s main strengths over other programming languages, e.g. execution speed and clarity of code, you should really get into the habit of putting everything in functions. But do whatever you prefer for now and note when you revisit this thread in a year or two that I told you so.