Вот мое решение, использующее библиотеку BouncyCastle.
// create the RSA key from an XML string
RSACryptoServiceProvider key = new RSACryptoServiceProvider();
key.FromXmlString(keyTextBox.Text);
// convert to BouncyCastle key object
var keypair = DotNetUtilities.GetRsaKeyPair(key);
var gen = new X509V3CertificateGenerator();
string certName = Path.GetFileNameWithoutExtension(fileName);
var name = new X509Name("CN=" + certName);
var serial = BigInteger.ProbablePrime(120, new Random());
gen.SetSerialNumber(serial);
gen.SetSubjectDN(name);
gen.SetIssuerDN(name);
gen.SetNotAfter(DateTime.Now.AddYears(10));
gen.SetNotBefore(DateTime.Now);
gen.SetSignatureAlgorithm("MD5WithRSA");
gen.SetPublicKey(keypair.Public);
// generate the certificate
var newCert = gen.Generate(keypair.Private);
// convert back to .NET certificate
var cert = DotNetUtilities.ToX509Certificate(newCert);
// export as byte array
byte[] certData = cert.Export(X509ContentType.Pfx);
File.WriteAllBytes(fileName, certData);