I would really like an answer to this issue. Yesterday I tried this, and I thought I would share my experience, and from that maybe get a little closer to a conclusive sollusion.
This is what I found out:
Fixing the eSATA drive to boot was not any problem, neither was installing Windows 7 (based on that your motherboard supports boot through eSATA).
I´ve tried disconnecting the eSATA-drive and use my DVD to repair startup,
botrec.exe /rebuildbcd, and none seems to help. Although when I run the
bootrec.exe /rebuildbcd it finds my Windows installation at
C:/Windows, but when I attempt to repair it, the cmd says "No element found".
The problem seems to be that if your motherboard makes the first boot hard drive the primary drive, it will install the MBR there. My drive has the capability of connect with USB 2.0, and when I do so, the MBR gets to the right drive (C:) and all is good.
One solution might be to make the eSATA drive second to primary, and press the key that gives you the choice to boot from another drive.
Sadly, no motherboard except those in laptops has this function.