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Lower your preview quality while sync-ing: that should speed the video render up closer to real time. Or make a 'proxy' video file at a low-res/high-compression, and include it as a guide layer. AE is not the 'right' place to do your audio work...but if this is the only problem you're having, then streamlining the video pipeline might get you what you need.
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Pre-rendering the keyed footage-- which a technical way of suggesting that you make the "QT with alpha," file you mention-- would speed up the AE or Ppro preview-rendering considerably. Or disable the keyer temporarily while synching in AE or Ppro.
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