NOTE: you don't need to change Matlab's JRE.
If you do not want to change the JRE then some of the TinyOS tools that you compile using your normal JDK might not run properly in Matlab. The only class that I noticed to have a problem was SerialForwarder, which uses javax/comm.jar. If you compile SerialForwarder with the standard 1.3.1_01 JDK and then try to run it in the JRE that comes with matlab, it might not be able to open the serial port, even if you put the comm.jar file in Matlab's classpath. If you don't want to change Matlab's JRE but want to use SerialForwarder, you can always run SerialForwarder from your shell instead of from Matlab (i.e. run SerialForwarder in the JRE that it was compiled for). The rest of the tutorial will still work and connect to that instance of SerialForwarder just fine.
If you do change your JRE, there is a small chance that it will cause some weird behavior in Matlab, especially if you are using a version older than MatlabVersion 6.5 (R13). This is because you are running Matlab in a JRE that it wasn't compiled for. The most likely symptom is that you get an endless stream of Java Clipboard exceptions spewing on your screen. Just cut and paste something, however, and these should go away. I've experienced no problems at all with R13,which was compiled for JRE 1.3.