The instructions in the Missal are silent regarding the posture of the faithful during the Communion Rite. Though after the Rite they may sit or kneel during the silence (# 43). A Bishop does have some authority to establish norms that do not violate universal norms. Other things being equal, it would seem the faithful should give due consideration and strive to follow these norms. 
 
However, the norm you have articulated does present a few practical issues. Most notably, it would seem that the elderly, and others with issues of physical stamina, might find it difficult to stand for so long. Also, it does make prayer difficult at a time that is often very precious to people for a quiet moment with the Lord. Given the rather hurried nature of most American liturgies, it seems unlikely that significant time will be reserved after all are seated for quiet prayer. 
 
Given that the local bishop does have the authority to request certain norms to be observed, I might encourage you to strive to listen to what he's teaching. Perhaps there is an issue that the local church is trying to address. While prayer certainly pleases the Lord, obedience pleases him even more. Scripture says, Sacrifice or offering you wished not, but ears open to obedience you gave me” (Ps 40:4) 
 
In terms of answering your question in an absolutely legal sense, while not a canonist, I suspect that this norm should be interpreted in the same way that the norm for receiving communion standing in this country is interpreted. While the norm requests, for the sake of unity, the faithful receive Communion standing, an exception is to be made for those who strongly prefer to receive kneeling. (GIRM #160) So it seems allowance needs to be made for the faithful who strongly prefer kneeling in silent prayer. 
 
As in all things, balance is required in understanding the nature of Holy Mass. Mass is essentially the communal act of Christ with all his people, it is not essentially a private devotion. However, times of silent prayer and reflection are often mentioned in the general norms. But frankly, with the rather hurried masses of modern times, periods of silent reflection are often nonexistent. In this sense, your concerns are understandable. 
 
I surely encourage you to stay in communion with your bishop, and to continue to raise your concerns.

So called “gluten free hosts” are not utterly free of all gluten. There are still some trace amounts. The US Bishops Conference allows the use of very low gluten hosts and urges additional caution by listing three reputable suppliers of them on the USCCB website. 
 
As for the Blessed Sacrament making someone sick, it is not the Sacrament that does so, but the “accidents.” While your acknowledgement of the True Presence is laudable, it is important to remember that Catholic teaching states that though the bread is transubstantiated, the “accidents” remain. 
 
The "accidents" are the physical attributes of the bread and wine ‐ that is, what can be seen, touched, tasted, or measured. These remain, though the substance of bread and wine change to become the Body, Blood, Soul and Divinity of Jesus. Hence it does not follow that one could not be affected by gluten in a consecrated Host, or by alcohol in the consecrated Blood, for these attributes remain to our senses.