I am not an expert on Apple's FileVault but I did work in IT security for a long time so I think I can make some general comments that may be of assistance.
Firstly, the article you reference seems clearly to be for a very specific type of attack. This is for reasonably sophisticated attackers who can access your computer while it is still turned on. That allows them to access the encryption key used for FileVault and bypass the encryption. The risk you are worried about possibly doesn't match this threat at all.
For instance, this threat doesn't seem to apply if your computer is turned off - I think the contents of memory can typically only be read for a few minutes after power off (there are technical articles on the web about this if you need to know more). Of course, your computer is a laptop and so it is battery powered and therefore it is not out of the question that a thief would be able to steal it while still on - pulling out the power won't shut it down. You need to consider whether this is a likely scenario, depending on how you use it, and if you think these attackers would be likely to attempt this type of exploit - as opposed to just nicking it at Cash Converters (insert name of local pawn shop).
Secondly, it is true that if you encrypt your whole disk it can affect things like backups, depending on how you do them. A change to one file affects the entire encrypted volume and this may result in much larger backups as the backup might have to copy your entire disk or home directory. However, as far as I can see FileVault is now a mature technology, we have many Macbooks at work using it and they seem to be fine.
I hope that's some helpful background and perhaps someone with more expertise in this area will also respond. Another thing worth mentioning is that you can create encrypted disk volumes using Disk Utility that are good for small quantities of sensitive information. This is how I have always done it. You avoid any possible problems with making your entire directory encrypted, and still get the same type of protection for your sensitive data. You can read http://support.apple.com/kb/HT1578?viewlocale=en_US&locale=en_US for more information on how to do that.
There are also several other useful threads relating to FileVault in Apple Discussions, for instance https://discussions.apple.com/message/17942614#17942614 . You should be able to see them on the right hand side of this page under "More Like This".
Hope that is helpful.