How should foreign words (with foreign characters) be written in English text?
The Times (not to be confused with the New York Times) style guide says:
foreign words Write in roman when foreign words and phrases have become essentially a part of the English language (eg, elite, debacle, fête, de rigueur, soirée); likewise, now use roman rather than italic, but retain accents, in a bon mot, a bête noire, the raison d'être. Avoid pretension by using an English phrase wherever one will serve. See accents
and
accents Give French, Spanish, Portuguese, German, Italian, Irish and Ancient Greek words their proper accents and diacritical marks; omit in other languages unless you are sure of them. Accents should be used in headlines and on capital letters. With Anglicised words, no need for accents in foreign words that have taken English nationality (hotel, depot, debacle, elite, regime etc), but keep the accent when it makes a crucial difference to pronunciation or understanding - café, communiqué, détente, émigré, façade, fête, fiancée, mêlée, métier, pâté, protégé, raison d'être; also note vis-à-vis. See foreign words, Spanish
http://www.timesonline.co.uk/tol/tools_and_services/specials/style_guide/article986724.ece
The ideal would be to preserve the word as it appears in its native language, but it is something that English-speakers are very lazy about. Anything that looks orthographically odd (i.e. has glyphs that aren't part of everyday English) stands out and is usually thought of as pretentious, so there is a strong social pressure to normalize. Ligatures in particular tend to unlink into their component letters (think of ß as a ligature in this respect), and missing characters translate in various slightly inconsistent ways.
If a word becomes common currency in English, it gets normalized over time. In particular, the accents fall off: writing "café" is considered a bit affected these days, and "rôle" has pretty much died out, for example.
The Chicago Manual of Style (16th edition), says that ligatures should be decomposed in Latin and transliterated Greek, as well as in words borrowed into the English lexicon. However, æ and œ should be used for Old English and French words respectively, when respectively in an Old English or French context.
There’s a whole chapter on foreign languages, but in general I’d preserve accents and “strange” letters when including words from foreign languages.
But it depends a lot on context as well. What kind of text are you writing, who is your audience? In an academic context the answer is usually pretty straightforward (just see how books and papers in relevant fields do it), but if you’re writing for a wider audience, simplifying may be prudent.