Relatively few Anabaptists were drowned for the practice re-baptizing, or for having been re-baptized (perhaps a few hundred total). And most of those drownings were actually carried out by RC rather than Protestant authorities. The most famous victim of early Protestant authorities was Felix Manz in Zürich (under Zwingli). The practice also disappeared fairly quickly among Protestants, as well as more gradually among RC's, precisely because there was a growing sense that it was indeed excessive and biblically suspect.
Some notable Protestant writings that still excoriated Anabaptist teachings while promoting a more lenient, or at least more humane approach to dealing with Anabaptists, include:
De Origine, Progressu, Sectis, Nominibus & Dogmatibus Anabaptistarum (republished as Englands warning by Germanies woes), by the German Reformed theologian Frederick Spanheim.
How many horrible and pernicious Tenets, and how hurtfull both to publique and private quietnesse, lye hidden as it were behinde a curtaine, under this simple name of Anabaptists. To whom we wish from the Lord with all our hearts, the knowledge, love, and practice of that truth which by the speciall grace of God is preserved in the Orthodox Churches; and therewithall both present and perpetuall happinesse. Neither doe we go about to stir up the Magistrate against those men; nor would we have any force offered to their consciences; but thinke those meanes onely ought to be used, which may conduce to the information of those that erre, the reproving of their errors, and confirmation of the truth, so farre as it may stand with Christian prudence and charity.
Anabaptism, the true fountaine of Independency, by the Scottish Presbyterian and Westminster Assembly commissioner Robert Baillie.
This is almost all I have to say of the second caution also, That in the greatest pangs of our zeal we never forget charity. It’s true, in this dead age, where zeal against error or vice is so rare, and where it is found, of so low a degree, that we need not draw it down by the mixture of any allaying adjunct; yet because in some it has, and in more it may exceed, that charity which the Lord will have joyned with it, we shall be loth to separate. When ever we have to doe, not only with them in whom we evidently see some rayes of the image of God, but with very hypocrites, whom we have but too good ground to suspect of counterfeiting; yet, for charities sake, let us give them (so far as evident verity will admit) a good construction: leaving the full account and certain search of them to the Lords further discovery, whether here or in his own day. In the mean time, for the sake of that grace and truth they carry in their face and mouth, let us deal so gently with them as may be; yea, when we have to do with the grossest sinners, let us never put off the bowels of pity and humanity to the worst of them. Who hath made us of a better metall? What sometimes have we been? What before all our trials be over, may yet escape us, or our children, or our dearest friends? Who knoweth how soon these wicked persons may receive mercy, and be rescued out of Satans bands? […] What ever indignation we are obliged to carry against the sin, yet we must pity the man; and if any censure spirituall or temporall, be inflicted upon him, this justice must flow from the fountain of love and desire, by that ordinary means to recover the person, or else the execution will be no lesse heavy to the inflicter, then to him on whom it is inflicted.
Many also recognized Anglicans as Protestants.