Is it permissible to cross out the name of Allah or the name of the Messenger (peace be upon him) with a pen so that the features of the letters do not appear, instead of burning it?

All that contains the names of Allah Almighty and the names of the Messengers must be respected, out of reverence for Allah's sanctities and rituals. It is recommended to respect everything written, but there is no harm in striking out the names of Allah or the Messengers or anything else held sacred by the Sharia, in order to protect them from insult or for a prevailing legitimate interest, as Uthman (may Allah be pleased with him) did with the Mushaf.