Using the output from mysqldiff.exe to transform database2 to match database1
As it appears on the manual, use the option --difftype=sql in order to obtain the results as ALTER TABLEs.

You have an example on a recent MySQL Performance Blog post:

$ mysqldiff --force --difftype=sql \
--server1=root:msandbox@127.0.0.1:21489 \
--server2=root:msandbox@127.0.0.1:21490 \
employees:employees