Guillaume,
It's hard to disagree your points. I do not blame Play for the behaviour as it's Ebean's part. What's more most of ORM's I was working with, are pretty similar - changing model's/property's name can be painful.
But in such case I have other suggestion: currently Play's evolutions with enabled DDL generation suggests re-applying the 1.sql evolution which also performs DOWNS by the way and in the effect it creates dangerous possibility to destroy data by the accident. One stupid mouse click in the middle of the night and developer is about to going to suicide himself ;) I know that's not possible to find golden mean without writing custom schema migration tool (and I know that's not a Play's job) however maybe it would be better if Play could prevent accidental data loosing.
My second idea is change of the Play's EbeanPlugin class. Instead creating the only one 1.sql in evolutions folder it could create full DDL in separate folder which is not auto-assumed as new evolution. Remember that if auto DDL generated is enabled there is no way to use custom evolutions and vice versa.
There could be separate file for each change (ie. named with current time marker), and to apply this, developer would need to copy its content and paste into his own 'manual' evolution (or prepare proper ALTERS, comparing with previous DDL, manually or with 3-rd party tool).
This solution will be easiest to implement and additionally it fits two goals: enabling coexisting the manual evolutions with auto DDLs + preventing accidents.
This is suggestion to Play's dev team, all I can do here is writing documentation describing the concept, but I think it's worth of considering.