I tried to run your code, and it's failing for me, and I'm not entirely certain where it is failing.  But you said it is working for you, but only outputing one value.  That would be becauase you only have the single value token being exported, and also, it's happening within the loop, so it's likely looping through each value and updating each one individually into the token, so at the end, you just have the last value in the token.

So why don't you try this:

Add this line prior to line 4 - it creates a string list variable named accountNameListVariable: 

List<string> accountNameListVariable = new List<string>();

Then, comment out line 32 where you are setting the token value (add // to the beginning so the script ignores it - this is a trick to test removal of the code without actually deleting it and potentially needing to re-type it if you want to add it back later.  After that line, add this code, that will take the groupName value that is currently accessed in the loop and add it into the accountNameListVariable list that we created earlier: 

accountNameListVariable.Add(groupName);

Finally, after line 39, add this line which will take everything included in the accountNameListVariable and output it to Workflow as a multi-value token named accountNameListToken: 

SetMultiValueToken("accountNameListToken", accountNameListVariable, false);

Final code should look like this: 

protected override void Execute()
        {
            // Write your code here. The BoundEntryInfo property will access the entry, RASession will get the Repository Access session
            List<string> accountNameListVariable = new List<string>();
            try
            {
                SecurityIdentifier EVERYONE_SID = new SecurityIdentifier("S-1-1-0");

                var trusteeList = Trustee.EnumAllWindowsAccounts(this.RASession).Select(account => account.Sid);

                foreach (var sid in trusteeList)
                {
                    AccountReference acctRef = new AccountReference(sid, this.RASession);
                    string accountName = acctRef.AccountName;

                    if (acctRef.TrusteeType == TrusteeType.WindowsAccount && !acctRef.IsUser)
                        continue; // Don't retrieve groups for other groups

                    try
                    {
                        EffectiveAccessTokenInfo tokenInfo = Trustee.GetEffectiveAccessTokenInfo(sid, this.RASession);
                        
                        foreach (var groupSid in tokenInfo.Groups)
                        {
                            if (groupSid == EVERYONE_SID)
                                continue;

                            AccountReference grp = new AccountReference(groupSid, this.RASession);
                            string[] groupNames = new string[] { grp.AccountName };

                            foreach (var groupName in groupNames)
                            {
                                //SetTokenValue(accountName, groupName);
                                accountNameListVariable.Add(groupName);
                            }
                        }
                    }
                    catch {}
                }
            }
            catch {}
            SetMultiValueToken("accountNameListToken", accountNameListVariable, false);
        }

As I said, I couldn't get the code to work myself, and I haven't spent the time to determine why - but based on your statement that it was working, only returning a single value, I think that these changes may work.