Based on the original article, the total bonuses paid vs number of employees who got a bonus pegs the average bonus award at something like $1400, not exactly a huge amount of money.
Comparing average government employee wage against national average income makes little sense, since it ignores locality and qualification level, as already pointed out. Also, we have no idea (based on what has been provided thus far) how IRS employees compare to the average government worker anyway.
The distinction that part of their annual pay is a bonus seems like a bit of a red herring. Would it be more acceptable if the pay scale was simply an $80k salary, rather than $78k with a possible $2k bonus? Having part of the compensation as a bonus could be retention-related, or other non-profit driven motivation, just as an example, not that it even matters really... total compensation is total compensation regardless of how it's broken down.
This whole story is a media frenzy that does a great job getting people stirred up about an agency we may not always like (who doesn't hate paying taxes?), but not much more.
With all of that said, suggestions about tax systems that are simpler or easier to manage, and the like, are perfectly valid and probably worthy of consideration and discussion (not specifically here however, as it ventures into prohibited topic territory)