Just keep a tight control on your Global Level Security options (client class creation, etc...), Class Level Security options (you can for instance, disable clients deleting _Installation entries. It's also common to disable user field creation for all classes.), and most important of all, look out for the ACLs.
Usually I use beforeSave triggers to make sure the ACLs are always correct. So, for instance, _User objects are where the recovery email is located. We don't want other users to be able to see each other's recovery emails, so all objects in the _User class must have read and write set to the user only (with public read false and public write false).
This way only the user itself can tamper with their own row. Other users won't even notice this row exists in your database.
One way to limit this further in some situations, is to use cloud functions. Let's say one user can send a message to another user. You may implement this as a new class Message, with the content of the message, and pointers to the user who sent the message and to the user who will receive the message.
Since the user who sent the message must be able to cancel it, and since the user who received the message must be able to receive it, both need to be able to read this row (so the ACL must have read permissions for both of them). However, we don't want either of them to tamper with the contents of the message.
So you have two alternatives: either you create a beforeSave trigger that checks if the modifications the users are trying to make to this row are valid before committing them, or you set the ACL of the message so that nobody has write permissions, and you create cloud functions that validates the user, and then modifies the message using the master key.
Point is, you have to make these considerations for every part of your application. As far as I know, there's no way around this.