Got it done. The solution is pretty straight forward.Just add all recipients certificates to the bouncy castle EnvelopedGenerator and encrypt.
/* Create the encrypter */
SMIMEEnvelopedGenerator encrypter = new SMIMEEnvelopedGenerator();
encrypter.addKeyTransRecipient((X509Certificate) recipient1Cert);
encrypter.addKeyTransRecipient((X509Certificate) recipient2Cert);
/* Encrypt the MimeMessage*/
MimeBodyPart encryptedPart = encrypter.generate(signedMessage,
SMIMEEnvelopedGenerator.RC2_CBC, "BC");
while decrypting just provide the recipient cert. If it is one of the encrypting certs, your message will be decrypted successfully.