Is it permissible to purchase a house through institutions that claim to operate according to Islamic formulas (murabaha), when the monthly installments are higher than those of usurious loans, or is it more preferable to deal with usurious banks, especially given the doubts surrounding the legitimacy of some of these institutions' transactions?

It is absolutely impermissible to deal with usurious banks, especially if the transaction is prohibited, such as usurious loans. As for dealing with Islamic institutions, there is no harm in it if the transaction adheres to Sharia guidelines, such as the institution selling a commodity for a deferred price. Profit in selling is permissible, and it does not matter if the profit is higher than usurious interest, because Allah has permitted trade and forbidden usury. The profit in trade is fixed, while usurious interests multiply.