Well, I guess there are two, or three, or even four sides to every story. Firstly, it depends on your composing style. If you are anything like me, you compose your piece and just keep adding and recreating and making it to your visionary. I agree...pencil and paper is not really the way to go for me. It takes forever, and then I have to check my work, etc. etc. However, when I attempt to put it on the computer, it is even harder, not only because I have just Finale Notepad (I do not recommend this software at all), but because I let the computer control what I write down. The best option for me is to hook up my computer to a keyboard, get some software, and play away. If you get a good software, it should write down what you want pretty close.
Now, of course, you could be the kind of person who is a computer composer. That's fine. For some people, composing on the computer allows them to hear what they want without the hassle of knowing the instrument. However, that is where the problem lies. Say you play the violin, but want to compose for trumpet. First, your software must be able to write it in concert pitch so it transposes to what you want. The main problem, however, is if you are not terribly familiar with the instrument, you do not know, oh, if this is ackward or hard for the player, or if that note is too high or too low. Yes, some softwares have tools to prevent you from composing too high or low for certain instruments, but without at least some background with the instrument you are composing for, you are shooting in the dark in terms of difficulty. For example, someone who plays the flute may not realize that on violin, from a low A note on the G string to a 3rd or 4th octave A note on the E string is somewhat ackward to hit.
As far as I know, I can't imagine a computer hurting your musicianship. But, on the other hand, I'm still 2 years from college, and another 4 before I become a composing major.
Emmy