Lyric discussion by Kaflerkta 

My take:

All men have secrets and here is mine so let it be known we have been through hell and high tide I can surely rely on you and yet you start to recoil heavy words are so lightly thrown but I'd still leap in front of a flying bullet for you

Morrissey confided to an old reliable friend who's he been through a lot with that he was gay.   The friend had a bad reaction to this.  Morrissey says inspite of his reaction he would do anything for the guy because he's that good of a friend to him.  He would even take a bullet for him.

So what difference does it make? so what difference does it make? it makes none, but now you have gone and you must be looking very old tonight

He's commenting to himself afterwards, what difference
does it make that he's gay?  There isn't any but
apparently it irked this guy so much it probably caused
him to prematurely age! (talk about dry humor)

The devil will find work for idle hands to do I stole and I lied, and why? because you asked me to but now you make me feel so ashamed because I've only got two hands well, I'm still fond of you (ha ha)

Apparently he's done all kinds of things for this friend that could have got him trouble.  Inspite of that his friend makes him feel ashamed for being a gay human being.  However, he still likes him as a friend but his opinion is obviously change (thus the ha ha at the end.) It's omitted for some reason in lyrics above but Moz does say it.

So what difference does it make? so what difference does it make? it makes none, but now you have gone and your prejudice won't keep you warm tonight

Pretty straight forward although the ending could have two meanings  His friend is prejudice of him being gay and apparently Moz even threw him out of his house or told him to take a walk.  Thus, he's out in the cold.  Or his friend's prejudice makes him cold and callous as a person.

Oh the devil will find work for idle hands to do I stole and then I lied just because you asked me to but now you know the truth about me you won't see me anymore well, I'm still fond of you (a ha ha)

But no more apologies no more apologies I'm too tired, I'm so very tired and I'm feeling very sick and ill today but I'm still fond of you (a ha ha)

Apparently the guy tried to apologize but if you are prejudice, then you are what you are, so why apologize for being what you are?  Even if you are prejudice, cold callous homophobic?
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