~悩んだが

[katafei]

社長からの指示なので悩んだが、この仕事はやはり断ることにした。

A sentence from last year's JLPT2, so no context....
(underlined words were to be transliterated)

I don't quite get the meaning...
社長からの指示 instructions coming from the boss
なので so, still
悩んだが am worried about, but...
この仕事はやはり断ることにした after all decided to turn down this job.

This is as far as I get, but I can't get a sentence that makes sense....

[Hyperworm]

悩む can mean to worry over something; to be in two minds over what to do and worry about the consequences of your decision.
１ 決めかねたり解決の方法が見いだせなかったりして、心を痛める。思いわずらう。
「進学か就職かで―・む」「恋に―・む若者」「人生に―・む」

[NocturnalOcean]

Yeah, the 悩む refers to how this person was to handle the instructions from the boss.
One should normally do what your boss tells you, but this person was possibly in doubt of whether to do them or not, but after nayamuing a bit, he decided to not do them.

[katafei]

Ah, I get it now. Thanks ppl ^^