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Yes,the new version of Spybot is safe to download.
Two Spybot's showing in add/remove programs was a very old issue,and you shouldn't get that problem again....

Is that error appearing with Spybot uninstalled,or did you reinstall since?

There is nowhere to download the individual files,that I know of.
You could try redownloading Spybot over the top of your current install.But,first,we should find out why there are two versions of...

Did you have Spybot 1.4 on your computer,then download a later version through updates?

Try following this,and see if it helps:
http://www.safer-networking.org/en/howto/uninstall.html