For a definition of "effectively" such that future lifespan >> 1000 years, yes. The uploading process as described will be that painful for everyone, so either:
a) Everyone will spend roughly the same amount of time getting over the pain, and I wouldn't miss much of significance or be specifically disadvantaged.
or
b) Being uploaded would afford us the capability to delete our memories of the pain; so, though it would be experienced, it wouldn't have to be remembered, reducing its overall effect.
This response assumes that the experience of the pain during the uploading process, even if remembered, wouldn't interfere significantly with the upload's fidelity to the previous brain state. In other words, we wouldn't be warped beyond recognition upon completing the upload.
I don't think you are interpreting the hypothetical as Prismatic intended. You split into two versions, one of which is an upload of you right before the pain starts. The other version (your brain undergoing something like very slow deconstruction) experiences a thousand years of agony.
I have been trying to absorb the Lesswrong near-consensus on cryonics/quantum mechanics/uploading, and I confess to being unpersuaded by it. I'm not hostile to cryonics; just indifferent, and having a bit of trouble articulating why the insights on identity that I have been picking up from the quantum mechanics sequence aren't compelling to me. I offer the following thought experiment in hopes that others may be able to present the argument more effectively if they understand the objection here.
Suppose that Omega appears before you and says, “All life on Earth is going to be destroyed tomorrow by [insert cataclysmic event of your choice here]. I offer you the chance to push this button, which will upload your consciousness to a safe place out of reach of the cataclysmic event, preserving all of your memories, etc. up to the moment you pushed the button and optimizing you such that you will be effectively immortal. However, the uploading process is painful, and because it interferes with your normal perception of time, your original mind/body will subjectively experience the time after you pushed the button but before the process is complete as a thousand years of the most intense agony. Additionally, I can tell you that a sufficient number of other people will choose to push the button that your uploaded existence will not be lonely.”
Do you push the button?
My understanding of the Lesswrong consensus on this issue is that my uploaded consciousness is me, not just a copy of me. I'm hoping the above hypothetical illustrates why I'm having trouble accepting that.