Well, I managed to get that working. Thanks to EJP for pointing in the right direction. Since Java 1.7 there are two additional properties in $JRE_HOME/lib/security/java.security:
jdk.certpath.disabledAlgorithms=MD2
Controls algorithms for certification path building and validation.
jdk.tls.disabledAlgorithms=MD5, SHA1, RC4, RSA keySize < 1024
JVM-wide algorithm restrictions for SSL/TLS processing, the one I was looking for. Notation is quite obvious here; it's possible to disallow certain algorithms or limit key sizes. Both properties are supported in Oracle JRE 7, Open JRE 7 and (surprisingly) IBM Java v7