Paul was not saying that the church - made up of both Gentile and Jewish believers - is Israel.
Yes, he was. You are missing that Paul contrasted two Israels.
Romans 9:6 It is not as though God’s word had failed. For not
all who are descended from Israel are
Israel. 7 Nor because they are
his descendants are they all
Abraham’s children. On the contrary, “
It is through Isaac that your offspring will be reckoned.” 8 In other words, it is not
the children by physical descent who are
God’s children, but it is
the children of the promise who are regarded as
Abraham’s offspring.
I color coded the text to show each of the two Israels. National Israel is in blue and spiritual Israel is in red.
What Paul indicated here is that there is an Israel besides national Israel that is comprised of "all who are descended from Israel". That other Israel is regarded as Abraham's spiritual offspring (seed) because it is comprised of God's children who are the children of the promise. When he said "it is through Isaac that your offspring will be reckoned" he was relating that to the Israel of which "not all who are descended from Israel" are part, so that relates to the other Israel as well.
So, based on what is written in Romans 9:6-8, the question then becomes who are those who are reckoned or called through Isaac and are God's children and the children of the promise who are regarded (counted) as Abraham's offspring (seed)?
We can determine that from other scripture by interpreting scripture with scripture.
As for what Paul meant when he said "it is through Isaac that your offspring will be reckoned" we can determine that from this passage.
Galatians 4:22 For it is written that Abraham had two sons, one by the slave woman and the other by the free woman. 23 His son by the slave woman was born according to the flesh, but his son by the free woman was born as the result of a divine promise. 24 These things are being taken figuratively: The women represent two covenants. One covenant is from Mount Sinai and bears children who are to be slaves: This is Hagar. 25 Now Hagar stands for Mount Sinai in Arabia and corresponds to the present city of Jerusalem, because she is in slavery with her children. 26 But the Jerusalem that is above is free, and she is our mother. 27 For it is written: "Be glad, barren woman, you who never bore a child; shout for joy and cry aloud, you who were never in labor; because more are the children of the desolate woman than of her who has a husband.” 28 Now you, brothers and sisters, like Isaac, are children of promise.
In this passage, Paul figuratively contrasts the old and new covenants and indicates that those who are under the new covenant, represented by the free woman, 'like Isaac, are children of promise". And he applies that to the Jew and Gentile believers in the church that he was writing to.
Who are the children of God that are also the children of the promise who are regarded as Abraham's spiritual offspring/seed? Paul tells us that here...
Galatians 3:26 So
in Christ Jesus you are all children of God through faith, 27 for all of you who were baptized into Christ have clothed yourselves with Christ. 28
There is neither Jew nor Gentile, neither slave nor free, nor is there male and female, for
you are all one in Christ Jesus. 29
If you belong to Christ, then you are Abraham’s seed, and heirs according to the promise.
Those who are the children of God and the children of the promise and counted as Abraham's seed are those who are in the church. So, that is who Paul is talking about in Romans 9:6-8 when he talks about the Israel of which not all who are descended from national Israel are part. He was talking about Spiritual Israel in that passage in contrast to National Israel. All believers, like Isaac, are the children of the promise and part of Spiritual Israel because of being children of God through faith and being regarded as Abraham's spiritual seed.