Heb 6:1 is not parallel to II Jn 9. A very literal rendering of the Greek from Berry’s Interlinear reads:
Wherefore, having left the discourse [logon] of the beginning of the Christ, to the full growth we should go on; not again a foundation laying of repentance from dead works, and faith in God;
The word translated “doctrine” in Heb 6:1 is “logon”. The word for “doctrine in II Jn 9 is “didache”. The two words are not synonomous. “Logos” is a saying or word. “Didache” is the act of teaching or that which is taught.
Here are how some other versions render Heb 6:1
ASV ¶Wherefore leaving the doctrine of the first principles of Christ, let us press on unto perfection; not laying again a foundation of repentance from dead works, and of faith toward God,
BBE ¶For this reason let us go on from the first things about Christ to full growth; not building again that on which it is based, that is, the turning of the heart from dead works, and faith in God,
CJB Therefore, leaving behind the initial lessons about the Messiah, let us go on to maturity, not laying again the foundation of turning from works that lead to death, trusting God,
DBY Wherefore, leaving the word of the beginning of the Christ, let us go on to what belongs to full growth, not laying again a foundation of repentance from dead works and faith in God,
NASU Therefore leaving the elementary teaching about the Christ, let us press on to maturity, not laying again a foundation of repentance from dead works and of faith toward God,
NIV Therefore let us leave the elementary teachings about Christ and go on to maturity, not laying again the foundation of repentance from acts that lead to death, and of faith in God,
If you look at the above translations, the BBE, CJB, NIV and NASU all use the phrase “about Christ” in Heb 6:1. That translation would be much more friendly to my understanding of II Jn 9 (the teaching about Christ) than the KJV’s rendering of Heb 6:1 that you quoted.
In Heb 6:1 there are certainly more things than just Christ. However, Heb 6:1 identifies the context as the first teachings about Christ and that certainly includes faith and repentance. The problem that I see with understanding II Jn 9 to include mercy is that it has to be read into the text. What the text says is “Whosoever goeth onward and abideth not in the teaching of Christ, hath not God”. There is no provision for mercy in this statement if you understand it to mean “the teaching Christ gave”. You are either obedient or else you are outside of God. There is no middle ground. You could theoretically ask God to forgive you, but the effect of the prayer would only last until you sinned by commission, omission, or ignorance. Should you stand before God unexpectedly and before you had a chance to ask for forgiveness, your status would be the sad state of being without God. Such a state of affairs is not what the Bible describes about God, but it is the logical outcome if II Jn 9 is understood to mean the teaching from Christ.