Keep your Smite Glyph. Seriously.
Disc as it is now needs two glyphs: PW:S and Penance. Apart from that the only sort of viable glyphs for PvE disc healing are Renew (which is bad), FHeal (this could help with your problem, I suppose) and PoH. I personally use PoH, and I barely ever cast the spell outside of Decimate scenarios. Actually, I think Decimate is easier dealt with with single-target heals because by the time an early cast Borrowed Time PoH actually hits chances are it's too late.
I usually don't top up people immediately when they're shielded. In any case, the shield glyph does heal some of that damage.
Also, and mind you I've been Disc since level 47 so I might be wrong on this, but I have never used Greater Heal in TBC/Wrath instances. You could glyph FHeal and just make that your primary tank heal and see how it goes.
And I think part of your problem is that you're using Holy Nova when you should conserve your mana a bit. For comparison: If I don't spam Holy Nova in a heroic, I come out at 90%+ mana in the end without using all my cooldowns. If I do use it a lot, I'll end up with 20% after having used at least two cooldowns to get some back.