Here's the problem with using words like "bro" (however jokingly): the problem is not with what you[0] are thinking when you read the word "bro", but with what other people, especially newcomers, are thinking. The locker-room atmosphere that stuff like this creates is a huge barrier to entry for a lot of people, women especially, who infer that on top of all the technically difficult stuff that everyone has to learn to be CS types, they'll also have to deal with a constant barrage of "you're not our kind" flung at them by the in-group. You personally may not be intending that as your message, but I assure you that your personal intent does not matter when you are using language that has been associated with exclusion and discrimination.[1]
The problem here, if this program is actually intended to be used, is that just typing in the command would be a constant reminder of an entire subculture that is widely seen as[2] putting up walls and doors that say "NO GIЯLS ALOUD" around the programming profession, an attempt to preserve privilege. Those of you suggesting an alias are either being disingenuous or missing the point entirely.
[0] Meaning individuals, of whatever gender/race/class/whatever, that are likely to be reading HN.
[1] If you don't believe me, ponder for a moment sentences like, "But I like Negroes just fine!" Language matters.
[2] Again, you might not mean to reference that when you use words like "brogrammer". But it's how an awful lot of us read it.
EDIT: Rereading other posts on this page, I should add that I almost certainly got the phrase "shame about the name" stuck in my head from reading dewitt's post. Four words, such a concise summary of my attitude! :)
EDIT 2: "they'll have" -> "that everyone has" to clarify argument. Thx vezzy-fnord.
In short, you can't imbue them with any prejudice that you yourself hold for a word. The word is theirs to use for its positive meaning. You cannot police this.
Some words have no positive meaning. This one does, please stay away.