It's strange to deprecate something when you can still achieve the same effect in some roundabout way?
Isn't that true for ALL APIs? You could always rewrite any deprecated API yourself, using sun.unsafe or JNI if it was needed, or even compile your own patched SDK fork.
The main intend behind deprecation is telling people "we don't want to support this anymore and you shouldn't be using it".
This is totally orthogonal to "you won't be able to replicate this behavior".
Regardless, the deprecation serves as prominent warning that the programmer is about to shoot themselves in the foot.
(I'm actually more surprised that stop() hasn't been removed after all this time.)
Java 9 has introduced an API to get the process ID but before that, there was no defined way to get it, though it is accessible in a roundabout way via the JMX API, but even then it is not guaranteed. JNI would be another alternative.