Can you please help me to understand the wisdom behind menstruation? Not the physiological, but the spiritual and Islamic wisdom behind it. For a practicing Muslim woman, it is nothing but a nuisance. It is spiritually demotivating because you are unable to offer Salah during this time so you feel so disconnected with Allah.
Is Salah not the most beloved act of worship to Allah? I read somewhere that because the women of Bani Israeel would go to the Masjid and cause fitna, so Allah punished them with menstruation.
In the Name of Allah, the Most Gracious, the Most Merciful.
As-salāmu ‘alaykum wa-rahmatullāhi wa-barakātuh.
Allah Ta’ala created women with their feminine characteristics. Allah says in the Quran:
لَا يُسْأَلُ عَمَّا يَفْعَلُ (القرآن 21: 23)
“Allah is not questioned of what He does.” (Al-Quran 21:23)
It is thus Fard upon us not to question the creation of Allah. It is sufficient for us to believe that Allah is Al-Hakeem (All Wise). Every act of Allah with every creation of His is based on the infinite wisdom of Allah. Menses in a woman has physical and spiritual benefits.
Here under are some heath benefits of menstruation:
- The very first menstrual period of a woman which is known as menarche, endows a woman to someday conceive a child. As a girl matures and enters puberty, the pituitary gland releases hormones that stimulate the ovaries to produce other hormones called estrogen and progesterone. These hormones have many effects on a girl’s body, including physical maturation, growth, and emotions. If a woman does not experience a menstrual period, most likely she will not be able to conceive a child in her life.
- Monthly periods work like a cleaning system in a woman’s body for her uterus in which the old uterine lining is removed in order to make way for the new cycle. The menstrual period also releases bacteria from inside the reproductive system and helps the body to discharge excess iron, which can help lower the risk of cardiovascular disease.
- Monthly periods slow down a women’s aging process.
- When women menstruate, the color, odor, and texture of the menstrual blood can provide invaluable information as to the well-being of the woman. Menstrual blood can offer early signs of developing illness and allow for the prevention of disease.
- The period follows a drop in progesterone, a hormone that encourages water retention and slows metabolism. Usually a day or two after the period starts, progesterone is low and most women lose water weight and metabolize carbs.
- A monthly period helps a woman maintain a healthy weight. 
These are some of the health benefits according our limited understanding and researches. However, only Allah knows the true wisdom behind women having menses.
As for your second query, menses initiated from the time of Hawwa Alaihas Salam (mother of mankind). However, at the time of Bani Israel, the women would cause fitna. As a result, Allah Subhanahu Wa Ta’ala merely increased their menses as a form of punishment. 
It is important to understand that there are two issues to an act of worship.
- Submission to Allah
- Form of worship
Salah, fasting, reciting of the Quran are various forms of worship. They are secondary to the spirit of worship which is submission to Allah. A believer first submits to Allah and His orders. Whatever Allah wants her to do, the person carries that out. The various forms of worship, Salah etc. are consequences of one’s submission to Allah. The forms of worship are secondary. Submission to Allah is the actual spirit of worship. If it is the order of Allah not to perform Salah, then abstaining from Salah is submission to the order of Allah and as an act of worship. One should not feel that in menses one is not worshipping Allah. In fact, the actual submission is carried out.
Nevertheless, while it is not permissible for a woman to fast, pray Salah or recite Quran, it is permissible for her to do various forms of Zikr and keep her connection with Allah even while she is in her menses. 
It is advisable for a woman in her menses to sit on the musallah during the Salah timings and make Zikr. This practice will maintain the spirituality even in menses.
And Allah Ta’āla Knows Best
Checked and Approved by,
Mufti Ebrahim Desai.
(Links checked on 2/5/2013)
 وَذَكَرَ فِي آخِرِ الْفَتَاوَى الظَّهِيرِيَّةِ أَنَّ حِكْمَتَهُ أَنَّ حَوَّاءَ لَمَّا رَأَتْ الدَّمَ أَوَّلَ مَرَّةٍ سَأَلَتْ آدَمَ فَقَالَ لَا أَعْلَمُ فَأُوحِيَ إلَيْهِ أَنْ تَتْرُكَ الصَّلَاةَ فَلَمَّا طَهُرَتْ سَأَلَتْهُ فَقَالَ لَا أَعْلَمُ فَأُوحِيَ إلَيْهِ أَنْ لَا قَضَاءَ عَلَيْهَا، ثُمَّ رَأَتْهُ فِي وَقْتِ الصَّوْمِ فَسَأَلَتْهُ فَأَمَرَهَا بِتَرْكِ الصَّوْمِ وَعَدَمِ قَضَائِهِ قِيَاسًا عَلَى الصَّلَاةِ فَأَمَرَهَا اللَّهُ تَعَالَى بِقَضَاءِ الصَّوْمِ مِنْ قِبَلِ أَنَّ آدَمَ أَمَرَهَا بِذَلِكَ مِنْ غَيْرِ أَمْرِ اللَّهِ تَعَالَى، وَفِي مِعْرَاجِ الدِّرَايَةِ أَنَّ سَبَبَ قَضَائِهِ تَرْكُ حَوَّاءَ السُّؤَالَ لَهُ وَقِيَاسُهَا الصَّوْمَ عَلَى الصَّلَاةِ فَجُوزِيَتْ بِقَضَائِهِ بِسَبَبِ تَرْكِ السُّؤَالِ (البحر الرائق شرح كنز الدقائق، ج1ص204، دار الكتاب الإسلامي)
كَانَ أَوَّلُ مَا أُرْسِلَ الحَيْضُ عَلَى بَنِي إِسْرَائِيلَ (صحيح البخاري، ج1ص66، دار طوق النجاة)
 (وَأَمَّا) حُكْمُ الْحَيْضِ وَالنِّفَاسِ فَمَنْعُ جَوَازِ الصَّلَاةِ، وَالصَّوْمِ، وَقِرَاءَةِ الْقُرْآنِ، وَمَسِّ الْمُصْحَفِ إلَّا بِغِلَافٍ، وَدُخُولِ الْمَسْجِدِ، وَالطَّوَافِ بِالْبَيْتِ (بدائع الصنائع في ترتيب الشرائع، ج1ص44، دار الكتب العلمية)
فكذا في حق حرمة القراءة على الحائض وهذا إذا قصدت القراءة فإن لم تقصدها نحو أن تقرأ الحمد لله رب العالمين شكراً للنعمة فلا بأس به (المحيط البرهاني في الفقه النعماني، ج1ص217، دار الكتب العلمية)